Description

Calculates polymorphic site rates over protein coding genes

Input

name:type
description
pattern

meta:map

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

bam:file

BAM file

*.bam

bai:file

BAM index file

*.bai

gff:file

GFF file used to extract protein-coding genes

*.gff

fasta:file

Optional fasta file to run on a subset of references in the BAM file.

.{fa,fasta,fas,fna}

Output

name:type
description
pattern

polymut

meta:map

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

*.txt:file

Polymut report in .txt format.

*.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

cmseq
MIT License

Set of utilities on sequences and BAM files

github.com/SegataLab/cmseq
maintainer
Github user maxibor
get in touch
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