Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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. Learn more

PostprocessGermlineCNVCalls Follow

1 comment

  • Avatar


    According to samtools documentation (, if any of the ALT alleles is a symbolic allele (<DUP> or <DEL>), then POS denotes the coordinate of the base preceding the
    polymorphism. Does the POS column in the output VCF files created by PostprocessGermlineCNVCalls refer to the first position of the duplication/deletion event or the preceeding base?

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk