Description

Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type

Input

name:type
description
pattern

meta

:map

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

bam

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

bai

:file

Index for BAM/CRAM/SAM file

*.{bai,crai,sai}

Output

name:type
description
pattern

flagstat

meta

:map

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

*.flagstat

:file

File containing samtools flagstat output

*.{flagstat}

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:type
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
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
abotyperatacseqbamtofastqcallingcardschipseqcircdnacircrnacutandrungenomeassemblerhgtseqhicarlncpipemagmapmetatdenovomethylongmethylseqnanoseqnascentpacsomaticphageannotatorradseqriboseqrnadnavarrnafusionrnaseqrnasplicernavarsammyseqscnanoseqsmrnaseqviralmetagenomeviralrecon
maintainers
Github user drpatelh
Github user matthdsm
get in touch
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