The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Hi GATK team,
I have a problem with (at least) one variant in my vcf output of GenotypeGVCF. This is the problematic variant:
1 899937 rs143296006 G T 8502.66 PASS AC=8;AF=0.800;AN=10;DB;DP=386;FS=0.000;GQ_MEAN=116.00;GQ_STDDEV=96.12;MLEAC=10;MLEAF=1.00;MQ=59.95;MQ0=0;NCC=7;QD=30.91;SOR=4.475;VQSLOD=2.43;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 0/0:0,0:13:0:0|1:899928_G_C:0,0,0 ./.:22,0:22 1/1:0,26:26:87:1|1:899928_G_C:1261,87,0 ./.:14,0:14 ./.:29,0:29 1/1:0,30:30:99:1|1:899928_G_C:1422,99,0 ./.:39,0:39 1/1:0,40:40:99:1|1:899928_G_C:1935,129,0 ./.:29,0:29 1/1:0,85:85:99:1|1:899928_G_C:3908,265,0./.:32,0:32 ./.:26,0:26
As can be observed, for sample 1, I have 0/0 genotype while actually there are not reads supporting that genotype (AD=0,0), am I correct on this? If I look for this position in the gvcf file of that sample, I can not find any line regarding to the position, this is normal? So I have two issues:
1) Why AD=0,0 stands for 0/0 GT?
2) Why in the gvcf there is no line regarding to this position?
Furthermore, If I visualize this position in IGV, with the recalibrated bam file, I see this (see attached picture, the first bam). So, in my opinion, this is clearly 1/1 genotype for my sample. Am I missing something? Also, If I see this position for sample2 (./.:22,0) at IGV (see attached picture, second bam), it is also a 1/1 genotype, not ./. . And in sample2.gvcf file I can see this:
1 899937 . G <NON_REF> . . END=899938 GT:DP:GQ:MIN_DP:PL 0/0:22:0:22:0,0,0
Why 0/0? ...
Sorry if I'm not explaining myself very clear.
Thanks in advance.