Description

Merge multiple fixmated, sorted SAM/BAM/CRAM and then mark duplicates

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

input_files (file)

BAM/CRAM/SAM files

*.{bam,cram,sam}

index_files (file)

BAM/CRAM/SAM index

*.{bai,csi,crai}

meta2 (map)

Groovy Map containing reference information e.g. [ id:'genome' ]

fasta (file)

Reference genome file

*.{fasta,fa,fna}

fai (file)

Index of the reference file the CRAM was created with (optional)

*.fai

gzi (file)

Index of the compressed reference file the CRAM was created with (optional)

*.gzi

Output

Name
Description
Pattern

bam

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.bam (file)

Sorted and duplicate marked BAM file

*.bam

cram

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.cram (file)

Sorted and duplicate marked CRAM file

*.cram

index

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.{csi,crai} (file)

Index file for the sorted and duplicate marked BAM

*.{csi,crai}

metrics

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.metrics (file)

Duplicate metrics file

*.metrics

versions_samtools

${task.process} (string)

The name of the process

samtools (string)

The name of the tool

samtools version | sed "1!d;s/.* //" (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

samtools (string)

The name of the tool

samtools version | sed "1!d;s/.* //" (eval)

The expression to obtain the version of the tool

Tools

samtools_merge Documentation

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

doi: 10.1093/bioinformatics/btp352License: MIT

samtools_markdup Documentation

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

doi: 10.1093/bioinformatics/btp352License: MIT
Pipelines with this module
asccgenomeassemblymetagenomeassembly
Authors