Description

Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that’s what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bams (file)

Sorted BAM/CRAM/SAM files

*.{bam,cram,sam}

indexes (file)

BAI/CRAI files

*.{bai,crai}

fai (file)

FASTA index

*.{fai}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

output (file)

Files generated by indexcov

bams (file)

Sorted ans indexed BAM or CRAM index (.crai) files

*.{bam,crai}
mantainer
Github user lindenb
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Tools

goleft
MIT

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

github.com/brentp/goleft10.1093/gigascience/gix090