The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
Last chance to register for the GATK workshop next week in Basel, Switzerland! http://www.sib.swiss/training/upcoming-training-events/training/gatk-workshop-lecture

Why did HaplotypeCaller report HET genotype for loci without reads supporting REF?

skblazerskblazer Posts: 18Member
edited November 2012 in Ask the GATK team

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

Post edited by Geraldine_VdAuwera on

Answers

Sign In or Register to comment.