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FilterMutectCalls 'haplotype' filter value assigned to variants with different PGT tag

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    Genevieve Brandt (she/her)

    Hi Francesco Mazzarotto,

    Yes, this does look like bug with the phasing. Could you send in a bug report with a small snippet of your files that recreate this issue? The instructions of how to do that are here: https://gatk.broadinstitute.org/hc/en-us/articles/360035889671.

    Let me know once you have uploaded your files and I will take a look.

    Best,

    Genevieve

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    Francesco Mazzarotto

    Hi Genevieve,

    many thanks for this. I have tried to upload the file multiple times (last attempt with a file called bug_report_fmazzarotto.tar.gz) but I am unable to say if the upload was successful as both Filezilla and the ftp upload via terminal behaved strangely (Filezilla said that the upload was successful but then placed it among the "failed transfers", and the terminal seems to get stuck on the message "150 Opening Binary Mode data Connection"). However, trying to re-upload the file without renaming it, I get a "overwrite permission denied" message, as if the previous upload actually worked. 
    Would you please be able to check if the file was actually uploaded?

    Best wishes

    Francesco

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    Genevieve Brandt (she/her)

    Thanks Francesco, it was successful. We'll take a look.

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    Brian Wiley

    I am also seeing this as well for version 4.2.1.0.  I will see if I can create bug report but it indicates to only do so if asked so let me know.

    I also get something like below for PGT:PID

    0|1:2720441_C_A
    1|0:2720441_C_A
    chrX    2720441 .       C       A       .       haplotype;orientation;weak_evidence     AS_FilterStatus=weak_evidence;AS_SB_TABLE=53,127|1,3;DP=189;ECNT=2;GERMQ=93;MBQ=20,20;MFRL=159,119;MMQ=60,60;MPOS=26;NALOD=1.78;NLOD=17.76;POPAF=6;ROQ=1;TLOD=3.2;AC=1;AN=2     GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB     0|1:83,4:0.048:87:48,0:20,3:0|1:2720441_C_A:2720441:10,73,1,3
    chrX    2720445 .       G       T       .       haplotype;orientation   AS_FilterStatus=SITE;AS_SB_TABLE=43,123|2,4;DP=181;ECNT=2;GERMQ=93;MBQ=30,20;MFRL=160,109;MMQ=60,60;MPOS=30;NALOD=1.75;NLOD=16.55;POPAF=6;ROQ=1;TLOD=6.37;AC=1;AN=2     GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB     1|0:79,6:0.062:85:41,3:24,0:1|0:2720441_C_A:2720441:7,72,2,4

     

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    Brian Wiley

    Genevieve Brandt (she/her)

    Am I able to access to see updates on the bug report as a viewer?  No big deal if I cannot view it though :)

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    Genevieve Brandt (she/her)

    Brian Wiley thanks for letting us know! We are taking a look at Francesco's bug report and will let you know if we need any information from you. We aren't able to share the data.

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    Genevieve Brandt (she/her)

    Brian Wiley Francesco Mazzarotto Thank you for the bug report Francesco! We were able to identify that the haplotype filter only identifies PID matches and does not look at the PGT. I opened an issue ticket so that we can get the haplotype filter working properly: https://github.com/broadinstitute/gatk/issues/7809

    Another aspect of this update is we are planning on making the --linked-de-bruijn-graph option on as default with Mutect2 because we think this will make the PGT more reliable and accurate.

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    Francesco Mazzarotto

    Hi Genevieve - thanks very much for this. Is there an approximate date for the update release?

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    Genevieve Brandt (she/her)

    Francesco Mazzarotto I don't have an estimate for when it will get done at this point. Our developers are really busy and there are other projects our developer team is actively working on before they take a look at this bug report.

    When I discussed this with the developers, they noted that the variants that have this filter seem like true negatives. I think you can still use this tool even with this issue persisting. 

    Let me know if you have any other concerns.

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