Description

Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

gvcf (file)

gVCF(.gz) file or to a GenomicsDB

*.{vcf,vcf.gz}

gvcf_index (file)

index of gvcf file, or empty when providing GenomicsDB

*.{idx,tbi}

intervals (file)

Interval file with the genomic regions included in the library (optional)

intervals_index (file)

Interval index file (optional)

fasta (file)

Reference fasta file

*.fasta

fai (file)

Reference fasta index file

*.fai

dict (file)

Reference fasta sequence dict file

*.dict

dbsnp (file)

dbSNP VCF file

*.vcf.gz

dbsnp_tbi (file)

dbSNP VCF index file

*.tbi

Output

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

Genotyped VCF file

*.vcf.gz

tbi (file)

Tbi index for VCF file

*.vcf.gz

versions (file)

File containing software versions

versions.yml
included in
rnadnavar sarek
authors
Github user santiagorevale Github user maxulysse
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

gatk4
BSD-3-clause

Genome Analysis Toolkit (GATK4)

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590