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

HaplotypeCaller not calling expected variants. VCF file is much smaller than expected.

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    Laura Gauthier

    Hi Shawn McMurtrey,

    It looks like this is not human data that you're processing.  For human data, where we have a very complete reference, I would expect 100X depth to be more than sufficient, but then again that's with ploidy 2 calling.  I can't speak to the expected heterozygosity for this reference and I don't have great intuition for how the lower coverage would affect your sensitivity, especially if you're using higher ploidy calling, but that is an effect we would expect to see in human data, though at coverages closer to 15-20X.  You might be able to use the GATK tool DepthOfCoverage to see if your decreased sensitivity is associated with coverage dropout in specific regions.

    -Laura

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