Description

Index SAM/BAM/CRAM 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}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bai (file)

BAM/CRAM/SAM index file

*.{bai,crai,sai}

crai (file)

BAM/CRAM/SAM index file

*.{bai,crai,sai}

csi (file)

CSI index file

*.{csi}

versions (file)

File containing software versions

versions.yml
included in
atacseq bacass bamtofastq callingcards chipseq circdna circrna createpanelrefs crisprseq cutandrun hgtseq hicar magmap metatdenovo methylseq nanoseq nascent pathogensurveillance phageannotator phaseimpute radseq raredisease readsimulator riboseq rnadnavar rnafusion rnaseq rnasplice rnavar sammyseq sarek scnanoseq smrnaseq ssds taxprofiler variantcatalogue viralintegration viralrecon
maintainers
Github user drpatelh
Github user ewels
Github user maxulysse
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 10.1093/bioinformatics/btp352