Description

Generate text pileup output for one or multiple BAM files. Each input file produces a separate group of pileup columns in the output.

Input

name:type
description
pattern

meta:map

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

input:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

intervals:file

Interval FILE

*.bed

meta2:map

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

fasta:file

FASTA reference file

*.{fasta,fa}

Output

name:type
description
pattern

mpileup

meta:map

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

*.mpileup.gz:file

mpileup file

*.{mpileup}

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
abotyperrnadnavarsarek
maintainers
Github user drpatelh
Github user joseespinosa
get in touch
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