GATK4 -Tabulate pileup metrics for inferring contamination

Description

Summarizes counts of reads that support reference, alternate and other alleles for given sites.

Parameters

Reference sequence () [human]
Chromosome names in my BAM file look like (1, chr1) [chr1]
Reference sequence () [human]
Chromosome names in my BAM file look like (1, chr1) [chr1]
Genomic intervals /String []
Interval padding (Integer) [0]
Use Variants VCF also for intervals (yes, no) [no]

Details

Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination.

The tool requires a common germline variant sites VCF, e.g. derived from the gnomAD resource, with population allele frequencies (AF) in the INFO field. This resource must contain only biallelic SNPs and can be an eight-column sites-only VCF. The tool ignores the filter status of the variant calls in this germline resource.

Based on GATK4 GetPileupSummaries tool. For more detailed information, see GATK documentation,

Output

References

This tool is based on the GATK4 package.

For instructions on citing GATK4, please see GATK FAQ