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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.