Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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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

GATK4 CombineGVCFs gives wrong allelic depth


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    Laura Gauthier

    Hi Bowen Jin,

    You'll note that in the GVCF the 2 in the AD field refers to the non-reference allele.  The behavior of the tool is as expected: it assigns the non-ref AD to every allele it sees that is not the reference.  Maybe not desirable, but expected.  If this is not what you want to happen, you can run the ReblockGVCF tool, which will zero out non-ref AD values and prevent them from being propagated when more alleles are discovered in joint calling.

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