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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

gatk-4.1.4.1 HaplotypeCaller -D parameter for MIXED type

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    Bhanu Gandham

    Is there another RSID at that site that you expect to see? If so can you please post that?

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    孙祺伟(Qiwei Sun)

    Yes, rs11679645 is also chr2:201915227, it is for T>C

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    孙祺伟(Qiwei Sun)

    Hi Bhanu,

    I get the information from dbsnp file. and this site have two rsID, we detect both of them,but the vcf only report one.

    dbsnp database:

    chr2 201915227 rs1394227290 T TAC,TATAC . PASS
    chr2 201915227 rs11679645 T C . PASS

    my result: chr2 201915227 rs1394227290 T C,TAC

    I wonder if the result like this "chr2 201915227 rs11679645,rs1394227290 T C,TAC" could be better?

    or there are some reason that GATK only choose one.

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    孙祺伟(Qiwei Sun)

    Could anybody help me to solve the problem?

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    Bhanu Gandham

    Hi,

     

    We are looking into this and will get back to you shortly.

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    孙祺伟(Qiwei Sun)

    Thank you Bhanu!

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    Bhanu Gandham

    Hi,

     

    We don't think this is a bug exactly, it is more of a design limitation. We are however trying to fix this issue here: https://github.com/broadinstitute/gatk/pull/6626

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