Description

Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

0 ()

1 ()

0 ()

1 ()

0 ()

1 ()

variants (file)

Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.

*.vcf.gz

variants_tbi (file)

Index file for the germline resource.

*.vcf.gz.tbi

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.