Description

Checks that all data in the set of input files appear to come from the same individual

Input

Name (Type)
Description
Pattern

meta (map)

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

input1 (file)

List containing 1 or more bam/vcf files or a file containing filepaths

*.{bam,vcf,vcf.gz,txt,fofn}

input2 (file)

Optional list containing 1 or more bam/vcf files or a file containing filepaths

*.{bam,vcf,vcf.gz,txt,fofn}

haplotype_map (file)

Haplotype map file

*.{txt,vcf,vcf.gz}

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

crosscheck_metrics (file)

Metrics created by crosscheckfingerprints

*.{crosscheck_metrics.txt}
author
Github user matthdsm
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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 https://github.com/broadinstitute/picard/