Description

Call somatic SNVs and indels via local assembly of haplotypes.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

0 ()

1 ()

0 ()

1 ()

0 ()

1 ()

germline_resource (file)

Population vcf of germline sequencing, containing allele fractions.

*.vcf.gz

germline_resource_tbi (file)

Index file for the germline resource.

*.vcf.gz.tbi

panel_of_normals (file)

vcf file to be used as a panel of normals.

*.vcf.gz

panel_of_normals_tbi (file)

Index for the panel of normals.

*.vcf.gz.tbi

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

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