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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

Variant calling in gene H19 disabled due to zero mapping quality

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    Genevieve Brandt

    Hi sirian,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

    For context, check out our support policy.

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    SkyWarrior

    Yes there is.

    1- You may want to use alt-aware mapping with  GRCh38 which needs the alt file to be with the genome files and latest bwa versions will take care of it.

    2- You may use a version of GRCh38 that only includes the main contigs and no other extras as recommended by Heng Li here --> https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use 

     

     

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    sirian

    Thanks for your reply. However the problem I had was due to an unplaced contig chr11_KI270721v1_random, not an alt contig. The alt-aware alignment does not deal with it. The primary assembly still contains both chr11 and chr11_KI270721v1_random, so the same mapping issue will occur.

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    SkyWarrior

    You are right. I overlooked that part. However 2nd solution should fix your problem since the recommended genome does not have any alt or random sequences present only chr1-22 XY and MT are present. If you still have doubts about it you can build your own GRCh38 with just those contigs using samtools.

    Another solution would be using b37 or GRCh37. I checked my samples and H19 locus is mapped properly there.

     

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    sirian

    Thanks!

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