Question: one variant's AD tag in VCF file shows 0,0
2
gravatar for sxzhuxu
21 months ago by
sxzhuxu40
sxzhuxu40 wrote:

I find a variant in my vcf file. This variant's DPis 232, however the AD is '0,0'. I can't understand why REF and ALT allele depth is zero. What does this mean?

I use GATK-Lite as my SNP caller.

chr21   44476000        .       C       CT      595.73  PASS    AC=1;AF=0.500;AN=2;DP=232;FS=0.852;HaplotypeScore=77.9709;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;QD=2.57;RPA=11,12;RU=T;STR;set=variant2      GT:AD:DP:GQ:PL    0/1:0,0:232:99:731,0,5227
snp • 770 views
ADD COMMENTlink modified 3 months ago by finswimmer9.8k • written 21 months ago by sxzhuxu40
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