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

]

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

meta (map)

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

]

flagstat (file)

File containing samtools flagstat output

*.{flagstat}

versions (file)

File containing software versions

versions.yml
included in
atacseq bamtofastq callingcards chipseq circdna circrna cutandrun hgtseq hicar magmap metatdenovo methylseq nanoseq nascent oncoanalyser phageannotator radseq riboseq rnadnavar rnaseq rnasplice rnavar sammyseq scnanoseq smrnaseq viralrecon
maintainer
Github user drpatelh
get in touch
Ask a question on Slack Open an issue on GitHub

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