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

meta (map)

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

]

stats (file)

File containing samtools stats output

*.{stats}

versions (file)

File containing software versions

versions.yml
included in
atacseq bamtofastq callingcards chipseq circdna circrna cutandrun hgtseq hicar metatdenovo methylseq nanoseq nascent radseq raredisease rnadnavar rnaseq rnasplice rnavar sarek smrnaseq taxprofiler viralrecon
authors
Github user drpatelh Github user FriederikeHanssen Github user ramprasadn
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.html 10.1093/bioinformatics/btp352