Description

Produces comprehensive statistics from SAM/BAM/CRAM file

Input

name:type
description
pattern

meta:map

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

]

input:file

BAM/CRAM file from alignment

*.{bam,cram}

input_index:file

BAI/CRAI file from alignment

*.{bai,crai}

meta2:map

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

fasta:file

Reference file the CRAM was created with (optional)

*.{fasta,fa}

Output

name:type
description
pattern

stats

meta:map

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

]

*.stats:file

File containing samtools stats output

*.{stats}

versions

versions.yml:file

File containing software versions

versions.yml

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
atacseq bamtofastq callingcards chipseq circdna circrna cutandrun hgtseq hicar magmap metatdenovo methylseq nanoseq nascent phageannotator radseq raredisease riboseq rnadnavar rnaseq rnasplice rnavar sammyseq sarek scnanoseq smrnaseq taxprofiler tbanalyzer viralrecon
maintainers
Github user drpatelh
Github user FriederikeHanssen
Github user ramprasadn
get in touch
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