Description

Generates a count of coverage of alleles

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_index (file)

BAM/CRAM/SAM index file

*.{bai,crai,sai}

loci (file)

loci file

*.{tsv}

fasta (file)

Input genome fasta file. Required when passing CRAM files.

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

alleleCount (file)

Allele count file

*.{alleleCount}

Tools

allelecounter
A-GPL 3.0

Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings)