How is the genotype calculated?

cafebluecafeblue Member
edited October 2013 in Ask the GATK team

the following lines are from the output of UnifiedGenotyper (ver: 2.5-2-gf57256b) with EMIT_ALL_SITES of my data:

<br /> chrI 4435 . A . 41.99 . AN=2;DP=54;MQ=21.36;MQ0=44 GT:DP 0/0:54<br /> chrI 4436 . A G,T 96 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-1.393;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.4679;MLEAC=1,1;MLEAF=0.500,0.500;MQ=21.36;MQ0=44;MQRankSum=1.393;QD=1.78;ReadPosRankSum=-1.741;SB=-1.503e+01 GT:AD:DP:GQ:PL 1/2:35,3,16:54:28:153,37,28,116,0,113<br /> chrI 4437 . A . 41.99 . AN=2;DP=54;MQ=21.36;MQ0=44 GT:DP 0/0:54<br /> chrI 4438 . A C 94.97 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.422;DP=54;Dels=0.00;FS=3.332;HaplotypeScore=13.3138;MLEAC=2;MLEAF=1.00;MQ=21.36;MQ0=44;MQRankSum=2.054;QD=1.76;ReadPosRankSum=-2.054;SB=-6.519e-03 GT:AD:DP:GQ:PL 1/1:50,3:54:9:127,9,0<br /> chrI 4439 . A . 41.99 . AN=2;DP=54;MQ=21.36;MQ0=44 GT:DP 0/0:54<br /> chrI 4440 . T G 85.02 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.214;DP=55;Dels=0.00;FS=6.990;HaplotypeScore=13.3138;MLEAC=1;MLEAF=0.500;MQ=21.17;MQ0=45;MQRankSum=2.166;QD=1.55;ReadPosRankSum=-1.580;SB=-2.050e+00 GT:AD:DP:GQ:PL 0/1:51,4:55:24:115,0,24<br /> chrI 4441 . G . 44.99 . AN=2;DP=57;MQ=22.61;MQ0=46 GT:DP 0/0:57<br />

it is very interesting that the genotype of the three sites (4436, 4438, 4440) are "1/2", "0/1" and "1/1" respectively, and the MLEAC and MLEAF are different with each other too, while the reference coverage is very high, and they are very close to each other.

My question is how is the genotype calculated, and why different genotypes are chosen in this issue but the reference coverage is very high?

Thanks,

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