modules/gatk4_combinegvcfs

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

gvcfgatk4vcfcombinegvcfsshort variant discovery

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/combinegvcfs

Description

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

Input

Name (Type)

Description

Pattern

`meta` (map)

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

`vcf` (file)

Compressed VCF files

*.vcf.gz

`vcf_idx` (file)

VCF Index file

*.vcf.gz.idx

`fasta` (file)

The reference fasta file

*.fasta

`fai` (file)

FASTA index file

*.fasta.fai

`dict` (file)

FASTA dictionary file

*.dict

Output

Name (Type)

Description

Pattern

`combined_gvcf` (file)

Compressed Combined GVCF file

*.combined.g.vcf.gz

`versions` (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

modules/gatk4_combinegvcfs

Description