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

Does GATK work on non-diploid organisms? Follow

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    Alyssa Phillips

    I had a quick question regarding the calculation of P(D|G) for polyploids. In GATK's article on how HaplotypeCaller calculates genotype likelihoods, it states that you assume the organism is diploid (two haplotypes) when calculating P(D|G) and that this feature will be generalized in future versions. Has this been resolved? If not, how might this bias the PL values?

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