Description

Condenses homRef blocks in a single-sample GVCF

Input

Name (Type)
Description
Pattern

meta (map)

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

]

gvcf (file)

GVCF file created using HaplotypeCaller using the ‘-ERC GVCF’ or ‘-ERC BP_RESOLUTION’ mode

*.{vcf,gvcf}.gz

tbi (file)

Index of the GVCF file

*.tbi

intervals (file)

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

fasta (file)

The reference fasta file

*.fasta

fai (file)

Index of reference fasta file

fasta.fai

dict (file)

GATK sequence dictionary

*.dict

dbsnp (file)

VCF file containing known sites (optional)

dbsnp_tbi (file)

VCF index of dbsnp (optional)

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

gvcf (file)

Filtered GVCF

*rb.g.vcf.gz

tbi (file)

Index of the filtered GVCF

*rb.g.vcf.gz.tbi
author
Github user nvnieuwk
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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/categories/360002369672s 10.1158/1538-7445.AM2017-3590