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# Low QD Value for Well-Supported High-Coverage SNPs- other annotations to use?

Posts: 9Member

Hello,

I am hoping to perform hard filtering on some variants from a sequencing project where, unfortunately, I do not have information from enough samples for VQSR. I was planning to filter on the QD value, but it seems to be very low for variants that seem reasonable. Example:

chr7    55249063 .       G       A       225     PASS
AC=1;AC1=1;AF=0.500;AF1=0.5;AN=2;BaseQRankSum=1.307;DP=4582;DP4=937,935,1299,1316;Dels=0.00;FQ=225;FS=0.323;


This variant is shown in IGV in the attached file- it looks to be a true positive, but because of the high depth, QD is very low. Based on the QD documentation, it looks as QD simply cannot be used to filter high-coverage data, since the value is QUAL/unfiltered depth.

Is there an alternative annotation that expresses the same measure, since QD is recommended in all the hard filtering documentation? Would GQ be a good substitute?

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• Posts: 9Member

Correct- these calls are produced with samtools mpileup. I will try to determine a better cutoff for this data. Thanks for your help!