Description

Condenses homRef blocks in a single-sample GVCF

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

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
Description
Pattern

0 ()

0 ()

Tools

gatk4 Documentation

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.

doi: 10.1158/1538-7445.AM2017-3590License: Apache-2.0
Authors