About BaseQRankSum

KenKen Posts: 3Member
edited September 2012 in Ask the GATK team

Hi,

In some of my calls, I have ID=BaseQRankSum, whereas in others, it isn't reported. I'm wondering what makes the unified genotyper call this for some SNPs but not for others. Also, in the documentation, it says this test cannot be done on homozygous sites: "bases of the alternate allele). Note that the base quality rank sum test can not be calculated for homozygous sites."

But this value is present at 1/1 sites for the GT field, which I understand it to be homozygous calls? e.g.

BaseQRankSum not called: chr1 5503270 . G A 1023.62 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=56.06;MQ0=0;QD=35.30;SB=-375.13 GT:AD:DP:GQ:PL 1/1:0,29:29:87.24:1057,87,0

BaseQRankSum called: chr1 6577241 . G A 1359.86 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.312;DP=43;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=59.13;MQ0=0;MQRankSum=1.692;QD=31.62;ReadPosRankSum=0.787;SB=-641.06 GT:AD:DP:GQ:PL 1/1:3,40:43:34.37:1393,34,0

Can someone help interpret this?

Many thanks, Ken

Post edited by Geraldine_VdAuwera on

Best Answer

  • ebanksebanks Posts: 684GATK Developer mod
    Answer ✓

    The documentation should really read: "Note that the base quality rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles." That should clarify things for you.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

Answers

  • ebanksebanks Posts: 684GATK Developer mod
    Answer ✓

    The documentation should really read: "Note that the base quality rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles." That should clarify things for you.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

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