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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

Missing Variants from Panel of Normals



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    Pamela Bretscher

    Hi Dave Sims,

    I am going to move your post into our Community Discussions -> General Discussion topic, as the somatic topic is for reporting bugs with GATK.

    You can read more about our forum guidelines and the topics here: Forum Guidelines.



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    Genevieve Brandt (she/her)

    Hi Dave Sims,

    The new method for creating the Panel of Normals is different than the previous method so we do expect that there would be differences. It sounds like you have seen this article, but I'll just point out a few parts that are especially helpful for the points you brought up here.

    Furthermore, we never liked how germline variants, which are handled in a more principled way with our germline filter, ended up as hard-filtered pon sites, so the panel of normals workflow now optionally excludes germline events from its output, keeping only technical artifacts.

    It seems like this is a good explanation for many of the differences you are seeing. The other part of the method that is important here is in Mutect2, it is setting --max-mnp-distance 0 which turns off mnps. So, it makes sense that these would not appear in your PON.

    If you have seen that these changes are negatively affecting your results and you want to bring up some abnormal results after running Mutect2 with this PON, will you share more information about those sites? We can then look into those to determine if there is a bug here or if it is expected.

    Thank you,


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