Description

Verify mate-pair information between mates and fix if needed

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM file

*.{bam}

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

bam (file)

mate-pair verified BAM file

*.{bam}
authors
Github user sateeshperi Github user mjcipriano Github user hseabolt
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

picard
MIT

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

broadinstitute.github.io/picard gatk.broadinstitute.org/hc/en-us/articles/360036713471-FixMateInformation-Picard- https://github.com/broadinstitute/picard