Description

Reports alignment summary statistics for a BAM/CRAM/SAM file

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

]

idxstats (file)

File containing samtools idxstats output

*.{idxstats}

versions (file)

File containing software versions

versions.yml
included in
atacseq bamtofastq callingcards chipseq circdna circrna cutandrun hgtseq hicar metatdenovo nanoseq nascent radseq rnadnavar rnaseq rnasplice rnavar smrnaseq ssds viralrecon
author
Github user drpatelh
get in touch
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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.html 10.1093/bioinformatics/btp352