Description

Select a subset of variants from a VCF file

Input

Name (Type)
Description
Pattern

meta (map)

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

vcf (list)

VCF(.gz) file

*.{vcf,vcf.gz}

vcf_idx (list)

VCF file index

*.{idx,tbi}

intervals (file)

One or more genomic intervals over which to operate

.intervals

Output

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

Compressed VCF file

*.selectvariants.vcf.gz

vcf_tbi (list)

VCF file index

*.{idx,tbi}

versions (file)

File containing software versions

versions.yml
included in
raredisease
maintainers
Github user mjcipriano
Github user ramprasadn
get in touch
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Tools

gatk4
Apache-2.0

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/360036362532-SelectVariants https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590