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 can't input the known variant from pooled samples



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    Gökalp Çelik

    Hi yangangli

    Are your samples haploid originally? If not then your ploidy value should be even higher than what you used. For regular diploid samples HaplotypeCaller uses ploidy value of 2 as default. 

    Also can you use the latest version of GATK to test your case? Version is quite old and there has been quite a bit of changes posted along the way. 

    I hope this helps. 


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    Thank you for your suggestions, they are very useful to me.

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