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

Handling different ploidy for male samples during joint genotyping

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    Gökalp Çelik

    Hi Rebeka Bató

    I sent out the link to the much requested feature's PR to GATK therefore you can check again later on it to see if it is merged or not. Although this is a much expected request by many with the current standing of GATK it is not impossible to perform such operation within multiple steps as you have indicated. 

    Our tools, GenomicsDBImport and GenotypeGVCFs are all ready for mixed ploidy setups therefore we expect you not to have too much trouble working your way out with male X and Y chromosomes. You can,

    1- Call male autosomes and X and Y separately and genotype them together though if you have too many samples we suggest you perform your genotyping in smaller scatters and merge them later

    2- Call male autosomes and X and Y separately and genotype them separately which is still fine for your needs. 

    I hope this helps.

    Regards. 

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