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Any statistic to measure the "degree' of heterozygosity per site?
I had a somewhat strange question to ask people and get some opinion and see if this makes sense. I've followed the bestpractice guide and now at a stage where I'm looking at my SNP vcf file any interpret the data. I've sequenced a non-model Drosophila specifically I've pooled a couple of progeny from a single line and sequenced the genome. I think this pooling is biting me back since the het sites I'm getting back are not exactly following the traditional definiton of hets and homozygous variation (ie. homozygosity (0%/100%) or heterozygosity (50%))
For example the het site found in the line below follows the traditional definition of heterozygosity (50%ref and 50%alt):
genome 1428318 . G A 392.68 PASS AC=1;AF=0.071;AN=14;BaseQRankSum=0.207;ClippingRankSum=-8.860e-01;DP=259;FS=3.192;MLEAC=1;MLEAF=0.071;MQ=60.00;MQ0=0;MQRankSum=0.697;QD=12.27;ReadPosRankSum=1.11 GT:AD:DP:GQ:PL 0/0:.:32:64:0,64,1395 0/0:.:43:99:0,120,1800 0/0:.:23:62:0,62,990 0/1:16,16:32:99:426,0,422 0/0:.:28:67:0,67,1080 0/0:.:56:99:0,99,1800 0/0:.:45:99:0,120,1800
But something like this site doesn't look like the traditional het site:
genome 1430207 . C T 608.68 PASS AC=1;AF=0.071;AN=14;BaseQRankSum=1.57;ClippingRankSum=-2.430e-01;DP=322;FS=1.962;MLEAC=1;MLEAF=0.071;MQ=60.00;MQ0=0;MQRankSum=0.172;QD=5.85;ReadPosRankSum=0.799 GT:AD:DP:GQ:PL 0/0:.:21:60:0,60,900 0/1:81,23:104:99:642,0,2872 0/0:.:40:62:0,62,1485 0/0:.:28:66:0,66,990 0/0:.:45:71:0,71,1620 0/0:.:24:64:0,64,990 0/0:.:60:92:0,92,1800
So from here is there any way to measure this difference? One thing I was thinking was for all het sites I was wondering if taking the ratio of the numbers reported for the PL field would be a statistic to look at the degree of heterozygosity per site. Specifically the ratio of PL for 0/0 and 1/1 genotype would be ~1 if there are 50% ref and 50% alt reads whereas a deviation from 1 would indicate otherwise. I was planning to plot this out and see if the ratios cluster around 1 or if it looks different. Would this be a wrong way of using the PL field and are there any other ways to see the so called "degree" of heterozygosit per site? I'm sorry if I sound too confusing.