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Homozygous VS Heterozygous

meharmehar Posts: 72Member

Hi,

I have two SNP calls as shown below:

chr1 86208198 . G C 903.25 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=0.117;DP=33;Dels=0.00;FS=6.463;HRun=0;HaplotypeScore=8.5544;MQ=43.69;MQ0=0;MQRankSum=-0.506;QD=27.37;ReadPosRankSum=0.272;SB=-414.82 GT:AD:DP:GQ:PL 1/1:2,30:33:18.60:936,19,0

chr16 14895239 . C T 671.60 . AC=1;AF=0.50;AN=2;BaseQRankSum=-0.582;DP=33;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.5317;MQ=53.44;MQ0=0;MQRankSum=0.970;QD=20.35;ReadPosRankSum=-0.711;SB=-292.79 GT:AD:DP:GQ:PL 0/1:3,30:33:6.39:701,0,6

The first SNP is categorized as 1/1 and the second SNP as 0/1. For both the SNP's the variant allele ratio are 30/32=0.9375 and 30/33=0.909 which are approximately equal and above 0.9. On what criteria one SNP is determined as 0/1 and the other as 1/1?

As per my knowledge both the SNPs should be 1/1. Could anyone comment the reason for this discrepancy?

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,565Administrator, GATK Developer admin

    Have a look at this article, some of the points may be applicable: http://www.broadinstitute.org/gatk/guide/article?id=1235

    If not and you still think there is a problem, could you please post what version of GATK you are using and the command line?

    Geraldine Van der Auwera, PhD

  • meharmehar Posts: 72Member

    Hi,

    The second point seems to be applicable i.e. depth reported in the VCF is the unfiltered depth. But, here i have considered the filtered depth and im still unclear about the call.

    I am using GATK version 2.4-9 and the command line is:

    java -jar GenomeAnalysisTK.jar -glm SNP -R ref.fasta -T UnifiedGenotyper -I in.bam -o out.vcf.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,565Administrator, GATK Developer admin

    Hmm. Could you run again on that interval using the latest version (2.6)? It would also help to see a screenshot of the pileup in IGV if possible.

    Geraldine Van der Auwera, PhD

  • meharmehar Posts: 72Member

    I have re-run it using GATK latest version and it called botht he SNPs as 1/1 and it looks fine. But what has been changed from the previous version to have a different call? Based on what criteria it calls as 1/1 or 0/1?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,565Administrator, GATK Developer admin

    We have made some improvements to the calling model and fixed some bugs that led to incorrect calls. The most important changes to each version are listed here: http://www.broadinstitute.org/gatk/guide/version-history

    Geraldine Van der Auwera, PhD

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