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.

  • imputation 3
  • vcf 2
  • genomics 2
  • bam 1
  • cram 1
  • sam 1
  • sort 1
  • VCF 1
  • bcftools 1
  • metrics 1
  • low-coverage 1
  • glimpse 1
  • concordance 1
  • bgen 1
  • VCFtools 1
  • impute-info 1
  • tags 1
  • impute 1
  • haploype 1
  • fasta 0
  • fastq 0
  • metagenomics 0
  • genome 0
  • index 0
  • alignment 0
  • reference 0
  • assembly 0
  • bed 0
  • gatk4 0
  • structural variants 0
  • variant calling 0
  • database 0
  • annotation 0
  • align 0
  • merge 0
  • filter 0
  • gff 0
  • map 0
  • bacteria 0
  • statistics 0
  • coverage 0
  • variants 0
  • qc 0
  • classification 0
  • nanopore 0
  • classify 0
  • quality control 0
  • download 0
  • gtf 0
  • cnv 0
  • split 0
  • MSA 0
  • taxonomy 0
  • k-mer 0
  • gfa 0
  • variant 0
  • taxonomic profiling 0
  • contamination 0
  • pacbio 0
  • sentieon 0
  • somatic 0
  • convert 0
  • conversion 0
  • clustering 0
  • count 0
  • binning 0
  • proteomics 0
  • quality 0
  • single-cell 0
  • ancient DNA 0
  • copy number 0
  • phylogeny 0
  • bedtools 0
  • contigs 0
  • trimming 0
  • mags 0
  • reporting 0
  • bisulfite 0
  • build 0
  • gvcf 0
  • isoseq 0
  • variation graph 0
  • kmer 0
  • graph 0
  • long reads 0
  • sv 0
  • rnaseq 0
  • bqsr 0
  • databases 0
  • indexing 0
  • methylation 0
  • methylseq 0
  • bisulphite 0
  • compression 0
  • long-read 0
  • illumina 0
  • table 0
  • consensus 0
  • protein 0
  • cna 0
  • picard 0
  • wgs 0
  • QC 0
  • depth 0
  • stats 0
  • visualisation 0
  • taxonomic classification 0
  • openms 0
  • phage 0
  • 5mC 0
  • imaging 0
  • antimicrobial resistance 0
  • demultiplex 0
  • mapping 0
  • sequences 0
  • serotype 0
  • tsv 0
  • DNA methylation 0
  • markduplicates 0
  • aDNA 0
  • histogram 0
  • structure 0
  • scWGBS 0
  • WGBS 0
  • searching 0
  • amr 0
  • protein sequence 0
  • pangenome graph 0
  • bins 0
  • pairs 0
  • cluster 0
  • base quality score recalibration 0
  • neural network 0
  • plot 0
  • matrix 0
  • haplotype 0
  • expression 0
  • samtools 0
  • metagenome 0
  • cooler 0
  • mmseqs2 0
  • validation 0
  • aligner 0
  • virus 0
  • LAST 0
  • completeness 0
  • biscuit 0
  • checkm 0
  • annotate 0
  • bwa 0
  • db 0
  • gzip 0
  • filtering 0
  • bisulfite sequencing 0
  • bcf 0
  • mappability 0
  • phasing 0
  • machine learning 0
  • transcript 0
  • repeat 0
  • iCLIP 0
  • damage 0
  • palaeogenomics 0
  • archaeogenomics 0
  • genotype 0
  • genotyping 0
  • newick 0
  • mag 0
  • decompression 0
  • bismark 0
  • umi 0
  • complexity 0
  • gene 0
  • mkref 0
  • hmmer 0
  • peaks 0
  • segmentation 0
  • ncbi 0
  • sketch 0
  • population genetics 0
  • spatial 0
  • ucsc 0
  • evaluation 0
  • example 0
  • transcriptome 0
  • msa 0
  • kraken2 0
  • hmmsearch 0
  • sequence 0
  • gff3 0
  • blast 0
  • germline 0
  • dedup 0
  • seqkit 0
  • prediction 0
  • duplicates 0
  • mirna 0
  • NCBI 0
  • mitochondria 0
  • bedGraph 0
  • prokaryote 0
  • demultiplexing 0
  • antimicrobial peptides 0
  • snp 0
  • deduplication 0
  • report 0
  • feature 0
  • antimicrobial resistance genes 0
  • differential 0
  • json 0
  • short-read 0
  • tumor-only 0
  • vsearch 0
  • pangenome 0
  • single 0
  • splicing 0
  • plasmid 0
  • cnvkit 0
  • kmers 0
  • scRNA-seq 0
  • multiple sequence alignment 0
  • low frequency variant calling 0
  • de novo assembly 0
  • concatenate 0
  • de novo 0
  • benchmark 0
  • 3-letter genome 0
  • sourmash 0
  • cat 0
  • view 0
  • call 0
  • query 0
  • microbiome 0
  • svtk 0
  • diversity 0
  • amps 0
  • gridss 0
  • merging 0
  • adapters 0
  • structural 0
  • riboseq 0
  • clipping 0
  • mem 0
  • profile 0
  • summary 0
  • arg 0
  • single cell 0
  • indels 0
  • interval 0
  • counts 0
  • profiling 0
  • distance 0
  • FASTQ 0
  • text 0
  • wxs 0
  • antibiotic resistance 0
  • idXML 0
  • csv 0
  • isolates 0
  • MAF 0
  • visualization 0
  • detection 0
  • coptr 0
  • ptr 0
  • tabular 0
  • deamination 0
  • fragment 0
  • kallisto 0
  • mutect2 0
  • extract 0
  • mpileup 0
  • xeniumranger 0
  • compress 0
  • palaeogenetics 0
  • bgzip 0
  • fastx 0
  • gsea 0
  • miscoding lesions 0
  • BGC 0
  • CLIP 0
  • fungi 0
  • hic 0
  • deep learning 0
  • read depth 0
  • biosynthetic gene cluster 0
  • cut 0
  • compare 0
  • bin 0
  • HMM 0
  • ganon 0
  • quantification 0
  • parsing 0
  • containment 0
  • preprocessing 0
  • microarray 0
  • interval_list 0
  • ccs 0
  • haplotypecaller 0
  • hmmcopy 0
  • paf 0
  • HiFi 0
  • happy 0
  • ancestry 0
  • bedgraph 0
  • genmod 0
  • ranking 0
  • enrichment 0
  • peak-calling 0
  • skani 0
  • reference-free 0
  • microsatellite 0
  • bigwig 0
  • SV 0
  • diamond 0
  • sample 0
  • sequencing 0
  • DNA sequencing 0
  • targeted sequencing 0
  • hybrid capture sequencing 0
  • copy number alteration calling 0
  • snps 0
  • mtDNA 0
  • rna 0
  • genome assembler 0
  • public datasets 0
  • phylogenetic placement 0
  • malt 0
  • STR 0
  • family 0
  • fgbio 0
  • matching 0
  • ngscheckmate 0
  • reads 0
  • ampir 0
  • circrna 0
  • archaeogenetics 0
  • ont 0
  • bcl2fastq 0
  • redundancy 0
  • ATAC-seq 0
  • telomere 0
  • image 0
  • union 0
  • normalization 0
  • pypgx 0
  • abundance 0
  • retrotransposon 0
  • resistance 0
  • chromosome 0
  • transcriptomics 0
  • propr 0
  • logratio 0
  • umitools 0
  • isomir 0
  • DNA sequence 0
  • add 0
  • clean 0
  • bedpe 0
  • chunk 0
  • benchmarking 0
  • plink2 0
  • pseudoalignment 0
  • variant_calling 0
  • complement 0
  • hidden Markov model 0
  • krona chart 0
  • RNA 0
  • rna_structure 0
  • fcs-gx 0
  • reports 0
  • fingerprint 0
  • bakta 0
  • PCA 0
  • prokka 0
  • notebook 0
  • rsem 0
  • dna 0
  • transposons 0
  • bacterial 0
  • cfDNA 0
  • duplication 0
  • bracken 0
  • mapper 0
  • npz 0
  • guide tree 0
  • ataqv 0
  • indel 0
  • amplicon sequencing 0
  • ambient RNA removal 0
  • bwameth 0
  • windowmasker 0
  • typing 0
  • polishing 0
  • fam 0
  • mzml 0
  • small indels 0
  • somatic variants 0
  • fai 0
  • neubi 0
  • subsample 0
  • sylph 0
  • amplify 0
  • SNP 0
  • macrel 0
  • organelle 0
  • mlst 0
  • gatk4spark 0
  • highly_multiplexed_imaging 0
  • wastewater 0
  • spark 0
  • mcmicro 0
  • converter 0
  • image_analysis 0
  • intervals 0
  • panel 0
  • DRAMP 0
  • bim 0
  • dictionary 0
  • entrez 0
  • scores 0
  • combine 0
  • comparisons 0
  • insert 0
  • krona 0
  • wig 0
  • replace 0
  • structural_variants 0
  • fastk 0
  • UMI 0
  • lineage 0
  • pangolin 0
  • covid 0
  • pan-genome 0
  • pairsam 0
  • repeat expansion 0
  • html 0
  • roh 0
  • virulence 0
  • amplicon sequences 0
  • aln 0
  • vrhyme 0
  • arriba 0
  • quality trimming 0
  • score 0
  • cut up 0
  • genome mining 0
  • kraken 0
  • fusion 0
  • dist 0
  • cool 0
  • microbes 0
  • lossless 0
  • long_read 0
  • dump 0
  • shapeit 0
  • untar 0
  • pileup 0
  • CRISPR 0
  • gene expression 0
  • prokaryotes 0
  • relatedness 0
  • bamtools 0
  • checkv 0
  • png 0
  • chip-seq 0
  • tabix 0
  • transcripts 0
  • genome assembly 0
  • atac-seq 0
  • survivor 0
  • ligate 0
  • eukaryotes 0
  • spaceranger 0
  • adapter trimming 0
  • uLTRA 0
  • RNA-seq 0
  • informative sites 0
  • kinship 0
  • identity 0
  • minimap2 0
  • uncompress 0
  • observations 0
  • cellranger 0
  • mkfastq 0
  • angsd 0
  • genomes 0
  • hi-c 0
  • deeparg 0
  • host 0
  • das_tool 0
  • miRNA 0
  • das tool 0
  • PacBio 0
  • C to T 0
  • unzip 0
  • genotype-based deconvoltion 0
  • nucleotide 0
  • archiving 0
  • remove 0
  • zip 0
  • chimeras 0
  • prefetch 0
  • popscle 0
  • phase 0
  • minhash 0
  • genetics 0
  • hlala 0
  • mash 0
  • zlib 0
  • hla_typing 0
  • mudskipper 0
  • hla 0
  • trancriptome 0
  • tama 0
  • pharokka 0
  • find 0
  • long terminal repeat 0
  • metamaps 0
  • corrupted 0
  • nacho 0
  • checksum 0
  • haplotypes 0
  • mask 0
  • transcriptomic 0
  • interactions 0
  • lofreq 0
  • mapcounter 0
  • retrotransposons 0
  • lift 0
  • salmon 0
  • kma 0
  • hlala_typing 0
  • functional analysis 0
  • serogroup 0
  • xz 0
  • regression 0
  • bloom filter 0
  • k-mer index 0
  • krakentools 0
  • reformat 0
  • refine 0
  • maximum likelihood 0
  • nanostring 0
  • function 0
  • gstama 0
  • mRNA 0
  • taxids 0
  • taxon name 0
  • iphop 0
  • krakenuniq 0
  • haplogroups 0
  • screen 0
  • COBS 0
  • barcode 0
  • ichorcna 0
  • bustools 0
  • primer 0
  • archive 0
  • pair 0
  • khmer 0
  • long terminal retrotransposon 0
  • gene set analysis 0
  • polyA_tail 0
  • instrain 0
  • gene set 0
  • pigz 0
  • interactive 0
  • standardise 0
  • read-group 0
  • differential expression 0
  • vg 0
  • salmonella 0
  • varcal 0
  • fusions 0
  • soft-clipped clusters 0
  • doublets 0
  • smrnaseq 0
  • leviosam2 0
  • anndata 0
  • RNA sequencing 0
  • vcflib 0
  • mirdeep2 0
  • rename 0
  • fixmate 0
  • gene labels 0
  • dict 0
  • collate 0
  • bam2fq 0
  • scaffolding 0
  • rtgtools 0
  • hostile 0
  • junctions 0
  • decontamination 0
  • runs_of_homozygosity 0
  • seqtk 0
  • transformation 0
  • scaffold 0
  • FracMinHash sketch 0
  • standardisation 0
  • taxonomic profile 0
  • standardization 0
  • otu tables 0
  • frame-shift correction 0
  • svdb 0
  • long-read sequencing 0
  • de novo assembler 0
  • small genome 0
  • signature 0
  • taxon tables 0
  • join 0
  • sequenzautils 0
  • cancer genomics 0
  • sequence analysis 0
  • Pharmacogenetics 0
  • pharmacogenetics 0
  • snpsift 0
  • snpeff 0
  • effect prediction 0
  • shigella 0
  • switch 0
  • ancient dna 0
  • Streptococcus pneumoniae 0
  • polish 0
  • contig 0
  • megan 0
  • tumor 0
  • nucleotides 0
  • graph layout 0
  • split_kmers 0
  • multiallelic 0
  • small variants 0
  • nextclade 0
  • removal 0
  • rgfa 0
  • msisensor-pro 0
  • tnhaplotyper2 0
  • micro-satellite-scan 0
  • msi 0
  • cnvnator 0
  • variation 0
  • instability 0
  • MSI 0
  • homoploymer 0
  • reformatting 0
  • spatial_transcriptomics 0
  • resolve_bioscience 0
  • profiles 0
  • orthology 0
  • GC content 0
  • parallelized 0
  • trgt 0
  • ampgram 0
  • SimpleAF 0
  • amptransformer 0
  • duplicate 0
  • Read depth 0
  • Duplication purging 0
  • purge duplications 0
  • MCMICRO 0
  • ome-tif 0
  • repeats 0
  • dereplicate 0
  • orthologs 0
  • library 0
  • preseq 0
  • adapter 0
  • GPU-accelerated 0
  • import 0
  • variant pruning 0
  • bfiles 0
  • image_processing 0
  • registration 0
  • mitochondrion 0
  • human removal 0
  • screening 0
  • cleaning 0
  • proportionality 0
  • ped 0
  • comparison 0
  • orf 0
  • tree 0
  • interval list 0
  • antibiotics 0
  • intersection 0
  • structural-variant calling 0
  • emboss 0
  • joint genotyping 0
  • gatk 0
  • deconvolution 0
  • bayesian 0
  • xenograft 0
  • graft 0
  • fasterq-dump 0
  • antismash 0
  • sra-tools 0
  • RNA-Seq 0
  • settings 0
  • version 0
  • NRPS 0
  • secondary metabolites 0
  • merge mate pairs 0
  • correction 0
  • reads merging 0
  • short reads 0
  • tab 0
  • metadata 0
  • immunoprofiling 0
  • trim 0
  • windows 0
  • simulate 0
  • authentication 0
  • blastn 0
  • allele-specific 0
  • awk 0
  • eido 0
  • blastp 0
  • format 0
  • filtermutectcalls 0
  • samplesheet 0
  • deseq2 0
  • rna-seq 0
  • realignment 0
  • BAM 0
  • validate 0
  • heatmap 0
  • artic 0
  • metagenomic 0
  • microbial 0
  • eigenstrat 0
  • evidence 0
  • panelofnormals 0
  • regions 0
  • spatial_omics 0
  • random forest 0
  • proteome 0
  • metagenomes 0
  • demultiplexed reads 0
  • aggregate 0
  • edit distance 0
  • RiPP 0
  • baf 0
  • cnv calling 0
  • calling 0
  • scatter 0
  • unaligned 0
  • gwas 0
  • CNV 0
  • norm 0
  • normalize 0
  • repeat_expansions 0
  • UMIs 0
  • eCLIP 0
  • microscopy 0
  • expansionhunterdenovo 0
  • genomad 0
  • intersect 0
  • duplex 0
  • HOPS 0
  • splice 0
  • concat 0
  • tbi 0
  • parse 0
  • reheader 0
  • gem 0
  • ChIP-seq 0
  • genome bins 0
  • allele 0
  • fetch 0
  • identifier 0
  • GEO 0
  • estimation 0
  • single cells 0
  • cvnkit 0
  • recombination 0
  • MaltExtract 0
  • vdj 0
  • htseq 0
  • overlapped bed 0
  • bioawk 0
  • unionBedGraphs 0
  • Escherichia coli 0
  • csi 0
  • deduping 0
  • decoy 0
  • multinterval 0
  • boxcox 0
  • tnseq 0
  • bases 0
  • shiftBed 0
  • resistance genes 0
  • slopBed 0
  • reverse complement 0
  • plastid 0
  • simulation 0
  • hmmfetch 0
  • clumping fastqs 0
  • parallel 0
  • resfinder 0
  • propd 0
  • decompose 0
  • subtract 0
  • sizes 0
  • Read coverage histogram 0
  • region 0
  • transmembrane 0
  • genome graph 0
  • smaller fastqs 0
  • install 0
  • rrna 0
  • comparative genomics 0
  • sorting 0
  • idx 0
  • rad 0
  • mutect 0
  • autozygosity 0
  • deep variant 0
  • update header 0
  • homozygosity 0
  • biallelic 0
  • structural variant 0
  • file manipulation 0
  • bam2fastx 0
  • bam2fastq 0
  • immcantation 0
  • airrseq 0
  • immunoinformatics 0
  • co-orthology 0
  • homology 0
  • spectral clustering 0
  • sequence similarity 0
  • bamtobed 0
  • gost 0
  • genotypegvcf 0
  • site frequency spectrum 0
  • maskfasta 0
  • joint-genotyping 0
  • sompy 0
  • chunking 0
  • peak picking 0
  • BCF 0
  • introns 0
  • gaps 0
  • transform 0
  • ancestral alleles 0
  • gprofiler2 0
  • derived alleles 0
  • tnfilter 0
  • jaccard 0
  • overlap 0
  • getfasta 0
  • genomecov 0
  • array_cgh 0
  • cytosure 0
  • closest 0
  • vector 0
  • genome statistics 0
  • sliding 0
  • clr 0
  • cellpose 0
  • refflat 0
  • gtftogenepred 0
  • ucsc/liftover 0
  • crispr 0
  • antibody capture 0
  • umicollapse 0
  • antigen capture 0
  • scRNA-Seq 0
  • multiomics 0
  • files 0
  • mkvdjref 0
  • upd 0
  • bedtobigbed 0
  • uniparental 0
  • disomy 0
  • snv 0
  • downsample 0
  • downsample bam 0
  • subsample bam 0
  • vcf2db 0
  • gemini 0
  • maf 0
  • lua 0
  • toml 0
  • hifi 0
  • genepred 0
  • bigbed 0
  • uniq 0
  • polya tail 0
  • polymorphic sites 0
  • polymorphic 0
  • detecting svs 0
  • short-read sequencing 0
  • polymut 0
  • svtk/baftest 0
  • baftest 0
  • countsvtypes 0
  • rdtest2vcf 0
  • rdtest 0
  • vcf2bed 0
  • decompress 0
  • fast5 0
  • bedgraphtobigwig 0
  • chromosome_visualization 0
  • duplicate removal 0
  • chromap 0
  • quality assurnce 0
  • Mycobacterium tuberculosis 0
  • chromosomal rearrangements 0
  • eucaryotes 0
  • coding 0
  • cds 0
  • transcroder 0
  • sequencing adapters 0
  • qa 0
  • vcfbreakmulti 0
  • deduplicate 0
  • alr 0
  • copyratios 0
  • adna 0
  • c to t 0
  • postprocessing 0
  • proteus 0
  • readproteingroups 0
  • tblastn 0
  • eigenvectors 0
  • hicPCA 0
  • snakemake 0
  • workflow 0
  • workflow_mode 0
  • createreadcountpanelofnormals 0
  • denoisereadcounts 0
  • geo 0
  • readwriter 0
  • dnamodelapply 0
  • dnascope 0
  • subtyping 0
  • Salmonella enterica 0
  • sorted 0
  • groupby 0
  • tnscope 0
  • chloroplast 0
  • confidence 0
  • blat 0
  • mapad 0
  • yahs 0
  • calder2 0
  • verifybamid 0
  • DNA contamination estimation 0
  • Assembly 0
  • construct 0
  • graph projection to vcf 0
  • domains 0
  • compartments 0
  • extractunbinned 0
  • linkbins 0
  • topology 0
  • sintax 0
  • vsearch/sort 0
  • usearch 0
  • copy number variation 0
  • long read alignment 0
  • pangenome-scale 0
  • all versus all 0
  • mashmap 0
  • wavefront 0
  • whamg 0
  • wham 0
  • cadd 0
  • copy-number 0
  • copy number analysis 0
  • gender determination 0
  • copy number alterations 0
  • raw 0
  • illumiation_correction 0
  • mgf 0
  • bclconvert 0
  • ATACseq 0
  • shift 0
  • ATACshift 0
  • http(s) 0
  • utility 0
  • setgt 0
  • jvarkit 0
  • translate 0
  • tar 0
  • tarball 0
  • targz 0
  • HLA 0
  • nucBed 0
  • vsearch/fastqfilter 0
  • AT content 0
  • nucleotide content 0
  • elfasta 0
  • elprep 0
  • controlstatistics 0
  • source tracking 0
  • emoji 0
  • quality_control 0
  • installation 0
  • doublet_detection 0
  • barcodes 0
  • doCounts 0
  • subsetting 0
  • fastqfilter 0
  • vsearch/dereplicate 0
  • significance statistic 0
  • xml 0
  • ATLAS 0
  • uniques 0
  • Illumina 0
  • functional 0
  • tag2tag 0
  • sequencing_bias 0
  • hashing-based deconvolution 0
  • rank 0
  • java 0
  • script 0
  • post mortem damage 0
  • svg 0
  • telseq 0
  • standard 0
  • haplotag 0
  • atlas 0
  • staging 0
  • mkarv 0
  • Staging 0
  • microRNA 0
  • multiqc 0
  • mass_error 0
  • search engine 0
  • poolseq 0
  • variant-calling 0
  • stardist 0
  • logFC 0
  • p-value 0
  • Read report 0
  • admixture 0
  • malformed 0
  • fix 0
  • paired reads re-pairing 0
  • regex 0
  • patterns 0
  • doublet 0
  • Immune Deconvolution 0
  • Bioinformatics Tools 0
  • Computational Immunology 0
  • catpack 0
  • prepare 0
  • mzML 0
  • taxonomic composition 0
  • adapterremoval 0
  • chip 0
  • CRISPRi 0
  • 16S 0
  • hhsuite 0
  • hmmpress 0
  • hmmscan 0
  • phylogenies 0
  • antimicrobial reistance 0
  • junction 0
  • contiguate 0
  • reference panel 0
  • reference compression 0
  • partitioning 0
  • updatedata 0
  • scvi 0
  • AMPs 0
  • solo 0
  • import segmentation 0
  • nuclear segmentation 0
  • cell segmentation 0
  • allele counts 0
  • relabel 0
  • nuclear contamination estimate 0
  • resegment 0
  • morphology 0
  • post Post-processing 0
  • metagenome assembler 0
  • model 0
  • scanpy 0
  • antimicrobial peptide prediction 0
  • run 0
  • plotting 0
  • regtools 0
  • leafcutter 0
  • amp 0
  • recovery 0
  • mgi 0
  • Staphylococcus aureus 0
  • affy 0
  • reference panels 0
  • identity-by-descent 0
  • decomposeblocksub 0
  • block substitutions 0
  • pdb 0
  • drug categorization 0
  • Read trimming 0
  • parquet 0
  • scimap 0
  • cell_phenotyping 0
  • machine_learning 0
  • bamUtil 0
  • bamtools/split 0
  • clahe 0
  • refresh 0
  • association 0
  • GWAS 0
  • case/control 0
  • yaml 0
  • associations 0
  • spatial_neighborhoods 0
  • Bayesian 0
  • n50 0
  • structural-variants 0
  • omics 0
  • biological activity 0
  • bamtools/convert 0
  • prior knowledge 0
  • tag 0
  • cell_barcodes 0
  • mygene 0
  • go 0
  • mouse 0
  • pile up 0
  • bacphlip 0
  • virulent 0
  • cell_type_identification 0
  • seqfu 0
  • lifestyle 0
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  • DNA damage 0
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  • reduced 0
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  • mcr-1 0
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  • ratio 0
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  • reference genome 0
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  • variant caller 0
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  • extractvariants 0
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  • mitochondrial 0
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  • genome summary 0
  • gfastats 0
  • Mykrobe 0
  • Salmonella Typhi 0
  • Sample 0
  • Haplotypes 0
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  • joint-variant-calling 0
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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.

01200

vcf tbi csi versions

bcftools:

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 plugin impute-info:

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

Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset.

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errors_cal errors_grp errors_spl rsquare_grp rsquare_spl versions

glimpse:

GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.

Imputation of genotypes using a reference panel

0123456

vcf versions

minimac4:

Computationally efficient genotype imputation

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

A set of tools written in Perl and C++ for working with VCF files

0100

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

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