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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

Panel of Normals - inconsistent filtering behavior

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4 comments

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    Anthony Dias-Ciarla

    Hi Paula Berry,

    Thank you for writing to the GATK forum! I hope that we can help you sort this out.

    I brought your inquiry to our developers and received some feedback and next steps to share with you.

    Could you please clarify whether or not you are using FilterMutectCalls? We don’t have any info from your post about FilterMutectCalls, where the filtering occurs.

    Once you clarify this, hopefully, we can help you further. I look forward to hearing back from you.

    Best,
    Anthony

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    Paula Berry

    Hi Anthony Dias-Ciarla, thank you for taking a look at this. We use Sentieon v.202010 to filter, where TNhaplotyper2 is the module where mutect2 is used, and TNfilter is filtermutect.

    The two below commands are what is used for the variant calling and PON filtering:

    sentieon/202010/libexec/driver -t 10 -r hs37d5_pms2_cl_ex12-end_masked.fa -i A015-F.bam --algo TNhaplotyper2 --pon pon.vcf.gz --min_base_qual 20 --tumor_sample A015-F A015-F_unfiltered.vcf
                    
    sentieon/202010/libexec/driver -r hs37d5_pms2_cl_ex12-end_masked.fa -t 10 --algo TNfilter --tumor_sample A015-F -v A015-F_unfiltered.vcf A015-F.vcf

    sample where variant got filtered out: 
    before filter: 
    chr1    11181327        .       C       T       .       PASS  GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB     0/1:57,2504:0.978:2561:28,1255:29,1188:0|1:11181327_C_T:11181327:30,27,1208,1296
    after filter:
    N/A

    sample where variant is kept:
    before filter:
    chr1    11181327        .       C       T       .       PASS     GT:AD:AF:DP:F1R2:F2R1:SB        0/1:342,1323:0.801:1665:157,644:184,658:155,187,651,672
    After filter:
    chr1    11181327        .       C       T       .       panel_of_normals GT:AD:AF:DP:F1R2:F2R1:SB        0/1:342,1323:0.801:1665:157,644:184,658:155,187,651,672


    Example Summary:
    chr1    11181327        .       C       T       .       panel_of_normals BETA=0.333,0.244;FRACTION=0.075
    total number before PON filtering:
    23

    number filtered out:
    21

    The ones that were left in were tagged "panel of normal" instead of filtered.

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    Anthony Dias-Ciarla

    Hi Paula Berry,

    Thank you for responding with this information! Regrettably, we do not support Sentieon; therefore, we cannot help you in that regard. I’d recommend locating the entity that supports the filter and submitting a help request there.

    To re-emphasize, I genuinely regret not being able to provide more helpful information on this issue. Thank you for being a valued member of the GATK community. 

    Please do not hesitate to reach back out in the future for any other GATK-related questions/problems that might arise.

    Best,
    Anthony

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    Anthony Dias-Ciarla

    Hi Paula Berry,

    We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

    Kind regards,

    Anthony​

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