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}

input1_index:file

List containing 1 or more bam/vcf files indexes

*.{bai,csi,crai,tbi}

input2:file

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

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

input2_index:file

List containing 1 or more bam/vcf files indexes

*.{bai,csi,crai,tbi}

haplotype_map:file

Haplotype map file

*.{txt,vcf,vcf.gz}

meta2:map

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

fasta:file

Reference genome file

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

Output

name:type
description
pattern

crosscheck_metrics

meta:map

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

*.crosscheck_metrics.txt:file

Metrics created by crosscheckfingerprints

*.{crosscheck_metrics.txt}

versions

versions.yml:file

File containing software versions

versions.yml

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/
Github user matthdsm
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