Why did HaplotypeCaller report HET genotype for loci without reads supporting REF?
Posted in Ask the GATK team | Last updated on 2012-11-14 16:04:05


Comments (3)

Hi GATK team,

When I checked closely by IGV, I found many of the loci, with all reads supporting variants, were reported as a HET genotype by HC.

After go back to the VCF result, I still don't understand why HC called this as a HET genotype, due to the ref's AD is 0, for example:

0/1:0,20:99:1069,0,1743

The whole line of this loci in VCF as below:

SCF1       47255   .       T       A       21688.96        .       AC=33;AF=0.500;AN=66;ActiveRegionSize=225;DP=264;EVENTLENGTH=0;FS=0.000;Haploty
peScore=73.8674;InbreedingCoeff=-0.8774;MLEAC=33;MLEAF=0.500;MQ=85.46;MQ0=0;NVH=5;NumHapAssembly=19;NumHapEval=12;QD=84.07;QDE=16.81;TYPE=SNP;extType=S
NP        GT:AD:GQ:PL     1/1:0,4:18:503,18,0     0/1:0,16:99:1732,0,2964 0/1:0,4:99:279,0,173    0/1:0,5:99:353,0,884    0/1:0,3:99:279,0,645    0/1:0
,4:99:270,0,584    0/1:0,19:99:1428,0,4290 0/1:0,7:99:388,0,794    0/1:0,3:99:302,0,391    0/1:0,15:99:1087,0,1165 0/1:0,6:99:529,0,1437   0/1:0,4:99:4
82,0,493    0/1:0,12:99:1245,0,2556 0/1:0,5:99:433,0,605    0/1:0,4:99:624,0,1135   0/1:0,3:99:362,0,1219   0/1:0,4:99:454,0,866    0/1:0,5:99:200,0,29
8    0/1:0,14:99:1846,0,1785 0/1:0,3:99:130,0,205    0/1:0,16:99:1453,0,999  0/1:0,15:99:757,0,866   0/1:0,12:99:939,0,518   0/1:0,10:99:697,0,758   0/
1:0,8:99:790,0,1319   0/1:0,9:99:748,0,1417   0/1:0,7:99:634,0,2198   0/0:0,6:63:0,63,1438    0/1:0,8:99:1029,0,1634  0/1:0,5:99:676,0,874    0/1:0,2:6
5:65,0,107     0/1:0,20:99:1069,0,1743 0/1:0,2:14:14,0,710

Best, SK


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