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

]

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

polymut (file)

Polymut report in .txt format.

*.txt
author
Github user maxibor
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Tools

cmseq
MIT License

Set of utilities on sequences and BAM files

github.com/SegataLab/cmseq