Description

filter/convert SAM/BAM/CRAM file

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

index{:bash}

:file

BAM.BAI/BAM.CSI/CRAM.CRAI file (optional)

*.{.bai,.csi,.crai}

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘test’ ]

fasta{:bash}

:file

Reference file the CRAM was created with (optional)

*.{fasta,fa}

qname{:bash}

:file

Optional file with read names to output only select alignments

*.{txt,list}

index_format{:bash}

:string

Index format, used together with ext.args = ‘—write-index’

bai|csi|crai

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

${prefix}.bam{:bash}

:file

optional filtered/converted BAM file

*.{bam}

cram{:bash}

meta{:bash}

:map

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

${prefix}.cram{:bash}

:file

optional filtered/converted CRAM file

*.{cram}

sam{:bash}

meta{:bash}

:map

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

${prefix}.sam{:bash}

:file

optional filtered/converted SAM file

*.{sam}

bai{:bash}

meta{:bash}

:map

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

${prefix}.${file_type}.bai{:bash}

:file

optional BAM file index

*.{bai}

csi{:bash}

meta{:bash}

:map

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

${prefix}.${file_type}.csi{:bash}

:file

optional tabix BAM file index

*.{csi}

crai{:bash}

meta{:bash}

:map

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

${prefix}.${file_type}.crai{:bash}

:file

optional CRAM file index

*.{crai}

unselected{:bash}

meta{:bash}

:map

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

${prefix}.unselected.${file_type}{:bash}

:file

optional file with unselected alignments

*.unselected.{bam,cram,sam}

unselected_index{:bash}

meta{:bash}

:map

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

${prefix}.unselected.${file_type}.{csi,crai}{:bash}

:file

index for the “unselected” file

*.unselected.{csi,crai}

versions_samtools{:bash}

${task.process}{:bash}

:string

Name of the process

samtools{:bash}

:string

Name of the tool

samtools --version | head -1 | sed -e "s/samtools //"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

Name of the process

samtools{:bash}

:string

Name of the tool

samtools --version | head -1 | sed -e "s/samtools //"{:bash}

:eval

The expression to obtain the version of the tool

Tools

samtools
MIT

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.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352
included in
alleleexpressionbamtofastqcircdnacircrnacreatepanelrefscutandrunhgtseqhicarhlatypingphaseimputeradseqrarediseasernadnavarrnafusionsammyseqsarekscnanoseqssdstaxprofilerviralrecon
maintainers
Github user drpatelh
Github user joseespinosa
Github user FriederikeHanssen
Github user priyanka-surana
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