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log10PError cannot be > 0, where does it see the log10PError field?

thondeboerthondeboer Redwood City, CA, USAMember ✭✭


I am seeing this error in the VariantSelect tool when I give it the output from Freebayes:

MESSAGE: The provided VCF file is malformed at approximately line number 54: BUG: log10PError cannot be > 0 : 1.0

But I cannot seem to find the field log10PError...

I am guessing it has something to do with another message I see in the LOG file:

WARN 16:47:46,872 VCFHeader - Found GL format, but no PL field. As the GATK now only manages PL fields internally automatically adding a corresponding PL field to your VCF header

Could it have something to do with that? Otherwise I cannot see what the issue is..

Here's line 54 it complains about...All the GL fields are negative as they should I thought...

1 11167546 . C A -1.85E-13 . AB=0.00168067;ABP=2569.72;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=1190;DPRA=0;EPP=7.35324;EPPR=124.679;GTI=0;HWE=-0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9672;NS=1;NUMALT=1;ODDS=1611.02;PAIRED=1;PAIREDR=1;RO=1188;RPP=3.0103;RPPR=2574.04;RUN=1;SAP=3.0103;SRP=126.572;TYPE=snp;XAI=0;XAM=0;XAS=0;XRI=1.71786e-05;XRM=0.000386983;XRS=0.000369804;technology.ILLUMINA=1 GT:DP:RO:QR:AO:QA:GL 0/1:1190:1188:46987:2:81:-7.695,-352.376,-4229.23




  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭

    The QUAL value is definitely bad: -1.85E-13 is not mathematically possible. Remember that the QUAL is phred-scaled (so it should be -10*log10 of that value).

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Thon,

    In future, could you please refer to Appistry for support? As you know, part of the point of the commercialization of GATK is to lower our support burden so we can focus more on development.

    Thanks for your cooperation!

  • thondeboerthondeboer Redwood City, CA, USAMember ✭✭

    Our support with Appistry run out and we have no longer a license with them...Since I am asking about GATK Lite I would hope this forum is still open to us commercial users.....

  • Mark_DePristoMark_DePristo Broad InstituteMember admin

    Hi Thondeboer,

    As soon as GATK 2.4 we will no longer support GATK 2.3, as per our usual practices. What this means is that when 2.4 releases our response will be "update to 2.4", and not provide you with any support on 2.3 or earlier. You are of course welcome to find resources to support GATK 2.3 (seqanswers is a particularly good venue) on the web at large.

  • thondeboerthondeboer Redwood City, CA, USAMember ✭✭

    Well...Is this a bug in 2.3 then? That was not clear from our answer...It showed the same behaviour in 1.6 so does not seem to be anything new...I am suspecting that the GL field is converted into a PL field and somehow the conversion got mangled, but this may be a problem in the VCF file I am using and not necessarily in GATK...VCF files are quite an open format...

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    In this case it sounds like it's not a bug in any version of the GATK, it's more like Freebayes is outputting a bad VCF file. VCF format is not all that open -- the spec is pretty straightforward for all the important stuff. But a lot of tools out there play fast and loose with the spec. In which case all the GATK can do is come to a screeching halt and say "whoa, I can't work with this".

  • wenluowenluo Member

    Hi thon,
    I run into the same bad formatted vcf file generated by freebayes with the less than 0 score. Just want to know what did you do with the freebayes vcf file in the end? Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    My recommendation is to tell the authors of Freebayes that their tool is outputting bad VCFs that are not compatible with other software, and ask them to fix the problem.

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