Available Modules
Modules are the building stones of all DSL2 nf-core blocks. You can find more info from nf-core website, if you would like to write your own module.
Annotation and Ranking of Structural Variation
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tsv unannotated_tsv vcf versions
Annotation and Ranking of Structural Variation
Run the alignment/variant-call/consensus logic of the artic pipeline
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results bam bai bam_trimmed bai_trimmed bam_primertrimmed bai_primertrimmed fasta vcf tbi json versions
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
generate VCF file from a BAM file using various calling methods
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vcf versions
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
This command replaces the former bcftools view caller. Some of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand. The original calling model can be invoked with the -c option.
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vcf tbi csi versions
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
Concatenate VCF files
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vcf tbi csi versions
Concatenate VCF files.
Compresses VCF files
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fasta versions
Create consensus sequence by applying VCF variants to a reference fasta file.
Converts certain output formats to VCF
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vcf_gz vcf bcf_gz bcf hap legend samples tbi csi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcftools Haplotype-aware consequence caller
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vcf tbi csi versions
Haplotype-aware consequence caller
Filters VCF files
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vcf tbi csi versions
Apply fixed-threshold filters to VCF files.
Index VCF tools
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csi tbi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
Apply set operations to VCF files
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results versions
Computes intersections, unions and complements of VCF files.
Merge VCF files
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vcf index versions
Merge VCF files.
Compresses VCF files
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vcf tbi stats mpileup versions
Generates genotype likelihoods at each genomic position with coverage.
Normalize VCF file
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vcf tbi csi versions
Normalize VCF files.
Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available.
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vcf tbi csi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available
Split VCF by chunks or regions, creating multiple VCFs.
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scatter tbi csi versions
Split VCF by chunks or regions, creating multiple VCFs.
Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.
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vcf tbi csi versions
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The setGT plugin sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.
Split VCF by sample, creating single- or multi-sample VCFs.
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vcf tbi csi versions
Split VCF by sample, creating single- or multi-sample VCFs.
Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.
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vcf tbi csi versions
Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.
Extracts fields from VCF or BCF files and outputs them in user-defined format.
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output versions
Extracts fields from VCF or BCF files and outputs them in user-defined format.
Reheader a VCF file
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vcf index versions
Modify header of VCF/BCF files, change sample names.
Sorts VCF files
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vcf tbi csi versions
Sort VCF files by coordinates.
Split a vcf file into files per chromosome
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split_vcf versions
Sort VCF files by coordinates.
Generates stats from VCF files
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stats versions
Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using plot-vcfstats.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
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vcf tbi csi versions
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
Beagle v5.2 is a software package for phasing genotypes and for imputing ungenotyped markers.
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vcf log versions
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
Convert a BED file to a VCF file according to a YAML config
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vcf versions
Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
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bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Calculate Jaccard statistic b/w two feature files.
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tsv versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Identifies common intervals among multiple (and subsets thereof) sorted BED/GFF/VCF files.
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bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.
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bed versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants
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vcf versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
Summarizes methylation or SNV information from a Biscuit VCF in a standard-compliant BED file.
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bed versions
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
convert2vcf.pl is command line tool to convert CNVnator calls to vcf format.
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vcf versions
Tool for calling copy number variations.
view function to generate vcfs
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vcf tsv xls versions
calling CNVs using read depth
Annotate a VEP annotated VCF with the most severe consequence field
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vcf versions
Custom module to annotate a VEP annotated VCF with the most severe consequence field
Annotate a VEP annotated VCF with the most severe pLi field
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vcf versions
Custom module to annotate a VEP annotated VCF with the most severe pLi field
structural-variant calling with cutesv
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vcf versions
DeepSomatic is an extension of deep learning-based variant caller DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and normal data, produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports somatic variants in a standard VCF or gVCF file.
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vcf vcf_tbi gvcf gvcf_tbi versions
(DEPRECATED - see main.nf) DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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vcf vcf_tbi gvcf gvcf_tbi versions
Transforms the input alignments to a format suitable for the deep neural network variant caller
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examples gvcf small_model_calls versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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vcf vcf_index gvcf gvcf_index versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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vcf vcf_tbi gvcf gvcf_tbi versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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report versions
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content.
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vcf versions
Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.
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vcf tbi versions
Filter, sort and markdup sam/bam files, with optional BQSR and variant calling.
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bam logs metrics recall gvcf table activity_profile assembly_regions versions
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4.
Filter variants based on Ensembl Variant Effect Predictor (VEP) annotations.
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output versions
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through task.ext.args.
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vcf tbi tab json report versions
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Estimate repeat sizes using NGS data
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vcf json bam versions
A haplotype-based variant detector
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vcf versions
Performs local realignment around indels to correct for mapping errors
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bam versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
Generates a list of locations that should be considered for local realignment prior genotyping.
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intervals versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
SNP and Indel variant caller on a per-locus basis
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vcf versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
Apply a score cutoff to filter variants based on a recalibration table. AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). Specifically, it applies filtering to the input variants based on the recalibration table produced in the first step by VariantRecalibrator and a target sensitivity value.
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Calculates the allele-specific read counts for allele-specific expression analysis of RNAseq data
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csv versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Apply a Convolutional Neural Net to filter annotated variants
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
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combined_gvcf versions
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Create a panel of normals constraining germline and artifactual sites for use with mutect2.
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering.
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vcf tbi stats versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Apply tranche filtering
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation.
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genomicsdb updatedb intervallist versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.
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vcf tbi versions
Genome Analysis Toolkit (GATK4)
Call germline SNPs and indels via local re-assembly of haplotypes
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vcf tbi bam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Creates an index for a feature file, e.g. VCF or BED file.
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index versions
Genome Analysis Toolkit (GATK4)
Left align and trim variants using GATK4 LeftAlignAndTrimVariants.
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Merges several vcf files
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Call somatic SNVs and indels via local assembly of haplotypes.
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vcf tbi stats f1r2 versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios
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intervals segments denoised versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Condenses homRef blocks in a single-sample GVCF
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vcf versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Select a subset of variants from a VCF file
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Splits reads that contain Ns in their cigar string
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bam versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF.
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annotated_vcf index versions
Genome Analysis Toolkit (GATK4)
Clusters structural variants based on coordinates, event type, and supporting algorithms
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clustered_vcf clustered_vcf_index versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Filter variants
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vcf tbi versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Extract fields from a VCF file to a tab-delimited table
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table versions
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
for annotating regions, frequencies, cadd scores
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vcf versions
Annotate genetic inheritance models in variant files
Score compounds
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vcf versions
Annotate genetic inheritance models in variant files
annotate models of inheritance
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vcf versions
Annotate genetic inheritance models in variant files
Score the variants of a vcf based on their annotation
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vcf versions
Annotate genetic inheritance models in variant files
Genotype Salmonella Typhi from Mykrobe results
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tsv versions
Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
Concatenates imputation chunks in a single VCF/BCF file ligating phased information.
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merged_variants versions
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
Ligatation of multiple phased BCF/VCF files into a single whole chromosome file. GLIMPSE2 is run in chunks that are ligated into chromosome-wide files maintaining the phasing.
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merged_variants versions
GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.
Tool for imputation and phasing from vcf file or directly from bam files.
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phased_variants stats_coverage versions
GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.
merge gVCF files and perform joint variant calling
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bcf versions
Tools for population-scale genotyping using pangenome graphs.
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vcf tbi versions
A graph-based variant caller capable of genotyping population-scale short read data sets while incorporating previously discovered variants.
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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bedpe bed versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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vcf versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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bedpe bed versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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high_conf_sv all_sv versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.
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high_conf_sv all_sv versions
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.
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fasta gff vcf stats phylip embl_predicted embl_branch tree tree_labelled versions
Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.
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vcf versions
gvcftools is a package of small utilities for creating and analyzing gVCF files
Somatic VCF Feature Extraction tool from hap.y.
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features versions
Haplotype VCF comparison tools
Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants.
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summary_csv roc_all_csv roc_indel_locations_csv roc_indel_locations_pass_csv roc_snp_locations_csv roc_snp_locations_pass_csv extended_csv runinfo metrics_json vcf tbi versions
Haplotype VCF comparison tools
Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py
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preprocessed_vcf versions
Haplotype VCF comparison tools
Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations.
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features metrics stats versions
Haplotype VCF comparison tools somatic variant comparison
Human mitochondrial variants annotation using HmtVar. Contains .plk file with annotation, so can be run offline
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vcf versions
Human mitochondrial variants annotation using HmtVar.
This tools takes a background VCF, such as gnomad, that has full genome (though in some cases, users will instead want whole exome) coverage and uses that as an expectation of variants.
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tsv versions
useful command-line tools written to show-case hts-nim
A Python application to generate self-contained HTML reports for variant review and other genomic applications
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report versions
Extract BED file from hts files containing a dictionary (VCF,BAM, CRAM, DICT, etc...)
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bed versions
Java utilities for Bioinformatics.
Convert VCF to a user friendly table
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output versions
Java utilities for Bioinformatics.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
Filtering VCF with dynamically-compiled java expressions
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vcf tbi csi versions
Java utilities for Bioinformatics.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
annotate VCF files for poly repeats
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vcf tbi csi versions
Java utilities for Bioinformatics.
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
Lofreq subcommand to call low frequency variants from alignments
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vcf versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
It predicts variants using multiple processors
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vcf tbi versions
Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's call-parallel programme predicts variants using multiple processors
Lofreq subcommand to remove variants with low coverage or strand bias potential
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vcf versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available
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vcf versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.
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vcf versions
LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms.
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. This script reformats inversions into single inverted sequence junctions which was the format used in Manta versions <= 1.4.0.
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vcf tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
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candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi diploid_sv_vcf diploid_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
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candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi diploid_sv_vcf diploid_sv_vcf_tbi somatic_sv_vcf somatic_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
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candidate_small_indels_vcf candidate_small_indels_vcf_tbi candidate_sv_vcf candidate_sv_vcf_tbi tumor_sv_vcf tumor_sv_vcf_tbi versions
Structural variant and indel caller for mapped sequencing data
Imputation of genotypes using a reference panel
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vcf versions
Computationally efficient genotype imputation
mirtop export generates files such as fasta, vcf or compatible with isomiRs bioconductor package
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tsv fasta vcf versions
Small RNA-seq annotation
SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA
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full_alignment info_txt snp_alignment snp_genome_alignment snpstatistics snptable snptable_snpeff snptable_uncertainty structure_genotypes structure_genotypes_nomissing json versions
Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files.
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corr_matrix matched all pdf vcf versions
NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.
NVIDIA Clara Parabricks GPU-accelerated variant calls annotation based on dbSNP database
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vcf versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant.
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vcf gvcf versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating GATK GenotypeGVCFs
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vcf versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller.
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vcf gvcf versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
NVIDIA Clara Parabricks GPU-accelerated gvcf indexing tool.
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gvcf_index versions
NVIDIA Clara Parabricks GPU-accelerated genomics tools
Genotype structural variants using paragraph and grmpy
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vcf json versions
Graph realignment tools for structural variants
Convert a VCF file to a JSON graph
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graph versions
Graph realignment tools for structural variants
Assigns all the reads in a file to a single new read-group
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bam bai cram versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
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bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collects hybrid-selection (HS) metrics for a SAM or BAM file.
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metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collect multiple metrics from a BAM file
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metrics pdf versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collect metrics from a RNAseq BAM file
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metrics pdf versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
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metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Checks that all data in the set of input files appear to come from the same individual
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crosscheck_metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Computes/Extracts the fingerprint genotype likelihoods from the supplied file. It is given as a list of PLs at the fingerprinting sites.
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vcf tbi versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Converts a FASTQ file to an unaligned BAM or SAM file.
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bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list
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bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Verify mate-pair information between mates and fix if needed
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bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Lifts over a VCF file from one reference build to another.
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vcf_lifted vcf_unlifted versions
Move annotations from one assembly to another
Locate and tag duplicate reads in a BAM file
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bam bai cram metrics versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Merges multiple BAM files into a single file
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bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Samples a SAM/BAM/CRAM file using flowcell position information for the best approximation of having sequenced fewer reads
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bam bai num_reads versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
changes name of sample in the vcf file
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vcf versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases
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intervals versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Sorts BAM/SAM files based on a variety of picard specific criteria
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bam versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Sorts vcf files
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vcf versions
Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format
Automatically improve draft assemblies and find variation among strains, including large event detection
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improved_assembly vcf change_record tracks_bed tracks_wig versions
Recodes plink bfiles into a new text fileset applying different modifiers
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ped map txt raw traw beagledat chrdat chrmap geno pheno pos phase info lgen list gen gengz sample rlist strctin tped tfam vcf vcfgz versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Import variant genetic data using plink2
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pgen psam pvar pvar_zst versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
Convert from VCF file to BGEN file version 1.2 format preserving dosages.
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bgen_file sample_file log_file versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner
PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.
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vcf max_cov bad_sites versions
Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available.
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result vcf lmix singlet_result singlet_vcf versions
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools
Build a normal database for coverage normalization from all the (GC-normalized) normal coverage files. N.B. as reported in https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html, it is advised to provide a normal panel (VCF format) to precompute mapping bias for faster runtimes.
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rds png bias_rds bias_bed low_cov_bed versions
Copy number calling and SNV classification using targeted short read sequencing
Run PureCN workflow to normalize, segment and determine purity and ploidy
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pdf local_optima_pdf seg genes_csv amplification_pvalues_csv vcf_gz variants_csv loh_csv chr_pdf segmentation_pdf multisample_seg versions
Copy number calling and SNV classification using targeted short read sequencing
Call SNVs/indels from BAM files for all target genes.
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vcf tbi versions
A Python package for pharmacogenomics research
QUILT is an R and C++ program for rapid genotype imputation from low-coverage sequence using a large reference panel.
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vcf tbi rdata plots versions
Read aware low coverage whole genome sequence imputation from a reference panel
Markup VCF file using rho-calls.
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vcf versions
Call regions of homozygosity and make tentative UPD calls.
Converts a PED file to VCF headers
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output versions
RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation
Plot ROC curves from vcfeval ROC data files, either to an image, or an interactive GUI. The interactive GUI isn't possible for nextflow.
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png svg versions
RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation
The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set
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tp_vcf tp_tbi fn_vcf fn_tbi fp_vcf fp_tbi baseline_vcf baseline_tbi snp_roc non_snp_roc weighted_roc summary phasing versions
RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation
The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by cluster_identifier
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meis_tab dels_tab vcf versions
Soft Clipped Read Alignment Mapper
Apply a score cutoff to filter variants based on a recalibration table. Sentieon's Aplyvarcal performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). Specifically, it applies filtering to the input variants based on the recalibration table produced in the previous step VarCal and a target sensitivity value. https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm
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vcf tbi versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Accelerated implementation of the Picard CollectVariantCallingMetrics tool.
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metrics summary versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
modifies the input VCF file by adding the MLrejected FILTER to the variants
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vcf index versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
DNAscope algorithm performs an improved version of Haplotype variant calling.
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vcf vcf_tbi gvcf gvcf_tbi versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper.
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vcf_gz vcf_gz_tbi versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Runs Sentieon's haplotyper for germline variant calling.
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vcf vcf_tbi gvcf gvcf_tbi versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Filters the raw output of sentieon/tnhaplotyper2.
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vcf vcf_tbi stats versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.
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orientation_data contamination_data contamination_segments stats vcf index versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.
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vcf index versions
Sentieonยฎ provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)
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log read_qual breakpoints_double read_alignments read_ids collapsed_dup loh all_vcf all_breakpoints_clusters_list all_breakpoints_clusters all_plots somatic_vcf somatic_breakpoints_clusters_list somatic_breakpoints_clusters somatic_plots versions
Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants.
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merged_variants versions
Fast and accurate method for estimation of haplotypes (phasing)
smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developed by Brent Pedersen.
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vcf versions
structural variant calling and genotyping with existing tools, but, smoothly
structural-variant calling with sniffles
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vcf tbi snf versions
Core-SNP alignment from Snippy outputs
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aln full_aln tab vcf txt versions
Rapid bacterial SNP calling and core genome alignments
Rapid haploid variant calling
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tab csv html vcf bed gff bam bai log aligned_fa consensus_fa consensus_subs_fa raw_vcf filt_vcf vcf_gz vcf_csi txt versions
Rapid bacterial SNP calling and core genome alignments
Genetic variant annotation and functional effect prediction toolbox
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cache versions
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
Genetic variant annotation and functional effect prediction toolbox
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vcf report summary_html genes_txt versions
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
Annotate a VCF file with another VCF file
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vcf versions
SnpSift is a toolbox that allows you to filter and manipulate annotated files
The dbNSFP is an integrated database of functional predictions from multiple algorithms
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vcf versions
SnpSift is a toolbox that allows you to filter and manipulate annotated files
Splits/Joins VCF(s) file into chromosomes
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out_vcfs versions
SnpSift is a toolbox that allows you to filter and manipulate annotated files
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
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tsv html versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
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extract versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
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html pairs_tsv samples_tsv versions
Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format.
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input rdata plots vcf bgen versions
Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
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vcf versions
Tandem repeat genotyper for long reads
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vcf tbi versions
Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation
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vcf vcf_tbi genome_vcf genome_vcf_tbi versions
Strelka calls somatic and germline small variants from mapped sequencing reads
Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs
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vcf_indels vcf_indels_tbi vcf_snvs vcf_snvs_tbi versions
Strelka calls somatic and germline small variants from mapped sequencing reads
Converts a bedpe file to a VCF file (beta version)
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vcf versions
Toolset for SV simulation, comparison and filtering
Filter a vcf file based on size and/or regions to ignore
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vcf versions
Toolset for SV simulation, comparison and filtering
Compare or merge VCF files to generate a consensus or multi sample VCF files.
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vcf versions
Toolset for SV simulation, comparison and filtering
Simulate an SV VCF file based on a reference genome
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parameters vcf bed fasta insertions versions
Toolset for SV simulation, comparison and filtering
Report multiple stats over a VCF file
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stats versions
Toolset for SV simulation, comparison and filtering
SVbenchmark compares a set of โtestโ structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity.
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fns fps distances log report versions
SVanalyzer: tools for the analysis of structural variation in genomes
The merge module merges structural variants within one or more vcf files.
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vcf tbi csi versions
structural variant database software
Query a structural variant database, using a vcf file as query
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vcf versions
structural variant database software
Count the instances of each SVTYPE observed in each sample in a VCF.
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counts versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Convert an RdTest-formatted bed to the standard VCF format.
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vcf tbi versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Convert SV calls to a standardized format.
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vcf versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Converts VCFs containing structural variants to BED format
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bed versions
Utilities for consolidating, filtering, resolving, and annotating structural variants.
Convert a VCF file to a BEDPE file.
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bedpe versions
Tools for processing and analyzing structural variants
SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data
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json gt_vcf bam versions
Compute genotype of structural variants based on breakpoint depth
SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample
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gt_vcf json versions
Bayesian genotyper for structural variants
A tool to standardize VCF files from structural variant callers
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vcf tbi versions
create tabix index from a sorted bgzip tab-delimited genome file
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tbi csi versions
Generic indexer for TAB-delimited genome position files.
A tool to detect resistance and lineages of M. tuberculosis genomes
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bam csv json txt vcf versions
Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data
Identify chromosomal rearrangements.
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vcf ploidy versions
Search for structural variants.
Create fasta consensus with TOPAS toolkit with options to penalize substitutions for typical DNA damage present in ancient DNA
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fasta vcf ccf log versions
This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The FASTA processing modules, the FASTQ processing modules, the GFF processing modules and the VCF processing modules.
Tandem repeat genotyping from PacBio HiFi data
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vcf bam versions
Tandem repeat genotyping and visualization from PacBio HiFi data
Merge TRGT VCFs from multiple samples
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vcf versions
Tandem repeat genotyping and visualization from PacBio HiFi data
Given baseline and comparison sets of variants, calculate the recall/precision/f-measure
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fn_vcf fn_tbi fp_vcf fp_tbi tp_base_vcf tp_base_tbi tp_comp_vcf tp_comp_tbi summary versions
Structural variant comparison tool for VCFs
Over multiple vcfs, calculate their intersection/consistency.
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consistency versions
Structural variant comparison tool for VCFs
Normalization of SVs into disjointed genomic regions
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vcf versions
Structural variant comparison tool for VCFs
The Java port of the VarDict variant caller
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vcf versions
Call variants for a given scenario specified with the varlociraptor calling grammar, preprocessed by varlociraptor preprocessing
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bcf_gz vcf_gz bcf vcf versions
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
Obtains per-sample observations for the actual calling process with varlociraptor calls
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bcf_gz vcf_gz bcf vcf versions
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
Convert VCF with structural variations to CytoSure format
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cgh versions
If multiple alleles are specified in a single record, break the record into several lines preserving allele-specific INFO fields
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vcf versions
Command-line tools for manipulating VCF files
Command line tools for parsing and manipulating VCF files.
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vcf versions
Command line tools for parsing and manipulating VCF files.
Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.
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vcf versions
Command-line tools for manipulating VCF files
List unique genotypes. Like GNU uniq, but for VCF records. Remove records which have the same position, ref, and alt as the previous record.
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vcf versions
Command-line tools for manipulating VCF files
A set of tools written in Perl and C++ for working with VCF files
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vcf bcf frq frq_count idepth ldepth ldepth_mean gdepth hap_ld geno_ld geno_chisq list_hap_ld list_geno_ld interchrom_hap_ld interchrom_geno_ld tstv tstv_summary tstv_count tstv_qual filter_summary sites_pi windowed_pi weir_fst heterozygosity hwe tajima_d freq_burden lroh relatedness relatedness2 lqual missing_individual missing_site snp_density kept_sites removed_sites singeltons indel_hist hapcount mendel format info genotypes_matrix genotypes_matrix_individual genotypes_matrix_position impute_hap impute_hap_legend impute_hap_indv ldhat_sites ldhat_locs beagle_gl beagle_pl ped map_ tped tfam diff_sites_in_files diff_indv_in_files diff_sites diff_indv diff_discd_matrix diff_switch_error versions
Constructs a graph from a reference and variant calls or a multiple sequence alignment file
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graph versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
Deconstruct snarls present in a variation graph in GFA format to variants in VCF format
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vcf versions
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.
decomposes multiallelic variants into biallelic in a VCF file.
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vcf versions
A tool set for short variant discovery in genetic sequence data
Decomposes biallelic block substitutions into its constituent SNPs.
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vcf versions
A tool set for short variant discovery in genetic sequence data
normalizes variants in a VCF file
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vcf fai versions
A tool set for short variant discovery in genetic sequence data
The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery.
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vcf tbi graph versions
A large variant benchmarking tool analogous to hap.py for small variants.
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report bench_vcf bench_vcf_tbi versions
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