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Old 02-21-2013, 04:23 PM   #1
Location: Bay Area

Join Date: Jan 2009
Posts: 24
Default Error when uisng Freebayes VCF output with GATK SelectVariants

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 from GATK SelectVariants:

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 be 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
Any ideas anyone?

Thon de Boer, Ph.D.
Director of Product Management, Software
Strand Life Sciences
548 Market Street, Suite 82804
San Francisco, CA 94104, USA
Pioneers in Discovery Research Informatics
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freebayes, gatk, vcf

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