Description

Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

Compressed VCF files

*.vcf.gz

vcf_idx{:bash}

:file

VCF Index file

*.vcf.gz.idx

fasta{:bash}

:file

The reference fasta file

*.fasta

fai{:bash}

:file

FASTA index file

*.fasta.fai

dict{:bash}

:file

FASTA dictionary file

*.dict

Output

name:type
description
pattern

combined_gvcf{:bash}

meta{:bash}

:file

Compressed Combined GVCF file

*.combined.g.vcf.gz

*.combined.g.vcf.gz{:bash}

:file

Compressed Combined GVCF file

*.combined.g.vcf.gz

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

gatk4
Apache-2.0

Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590
included in
rnavar
maintainers
Github user sateeshperi
Github user mjcipriano
Github user hseabolt
Github user maxulysse
get in touch
Ask a question on Slack Open an issue on GitHub