[Useq-users] Fwd: Useq-users post from peter.white@nationwidechildrens.org requires approval

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Subject: Useq-users post from pet...@na...<mailto:pet...@na...> requires approval
Date: March 6, 2014 at 4:38:33 AM MST
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   From:    pet...@na...<mailto:pet...@na...>
   Subject: The floating point in GQ is causing an error
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From: "White, Peter" <Pet...@na...<mailto:Pet...@na...>>
Subject: The floating point in GQ is causing an error
Date: March 6, 2014 at 4:17:37 AM MST
To: "'use...@li...<mailto:use...@li...>'" <use...@li...<mailto:use...@li...>>

I receive this error when running the following command:

java -jar -Xmx22g USeq_8.7.6/Apps/VCFComparator -a GIAB_2.18.vcf -b GIAB_2.18.bed -c test.vcf -d GIAB_2.18.bed -p results

It seems to be listing every record as having an issue with the GQ field:

Skipping malformed VCF Record-> chr1    28563   .       A       G       747.81  TruthSensitivityTranche99.90to100.00    AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=27.68;MQ0=0;QD=23.37;SB=-344.16;VQSLOD=-4.1666;culprit=MQ        GT:DP:GQ:PL 1/1:32:83.94:781,84,0
Error-> For input string: "83.94"
Skipping malformed VCF Record-> chr1    28663   .       T       A       135.07  TruthSensitivityTranche99.90to100.00    AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=21.88;MQ0=0;QD=19.30;SB=-0.01;VQSLOD=-6.8165;culprit=DP   GT:DP:GQ:PL1/1:7:18.02:168,18,0
Error-> For input string: "18.02"

Aborting, problem parsing vcf file -> churchill.vcf
java.lang.Exception:
Too many malformed VCF Records.

        at edu.utah.seq.vcf.VCFParser.parseVCF(VCFParser.java:229)
        at edu.utah.seq.vcf.VCFParser.<init>(VCFParser.java:136)
        at edu.utah.seq.vcf.VCFComparator.parseFilterFiles(VCFComparator.java:436)
        at edu.utah.seq.vcf.VCFComparator.<init>(VCFComparator.java:69)
        at edu.utah.seq.vcf.VCFComparator.main(VCFComparator.java:515)

Any ideas what might be causing it?

Thanks,

Peter

Peter White, Ph.D.
Principal Investigator, Center for Microbial Pathogenesis<http://www.nationwidechildrens.org/microbial-pathogens>
Director, Biomedical Genomics Core<http://genomics.nchresearch.org/>
Director of Molecular Bioinformatics, The Research Institute at Nationwide Children's Hospital<http://www.nationwidechildrens.org/pediatric-research>
Assistant Professor of Pediatrics, The Ohio State University<http://pro.osumc.edu/profiles/white.1586/>

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