Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

input1{:bash}

:file

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

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

input1_index{:bash}

:file

List containing 1 or more bam/vcf files indexes

*.{bai,csi,crai,tbi}

input2{:bash}

:file

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

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

input2_index{:bash}

:file

List containing 1 or more bam/vcf files indexes

*.{bai,csi,crai,tbi}

haplotype_map{:bash}

:file

Haplotype map file

*.{txt,vcf,vcf.gz}

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

fasta{:bash}

:file

Reference genome file

*.{fasta,fa,fasta.gz,fa.gz}

Output

name:type
description
pattern

crosscheck_metrics{:bash}

meta{:bash}

:map

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

*.crosscheck_metrics.txt{:bash}

:file

Metrics created by crosscheckfingerprints

*.{crosscheck_metrics.txt}

versions_picard{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

picard{:bash}

:string

The tool name

picard CrosscheckFingerprints --version 2>&1 | sed -n 's/.*Version://p'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

picard{:bash}

:string

The tool name

picard CrosscheckFingerprints --version 2>&1 | sed -n 's/.*Version://p'{:bash}

:string

The command used to generate the version of the tool

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/
maintainer
Github user matthdsm
get in touch
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