one variant's AD tag in VCF file shows 0,0
0
2
Entering edit mode
6.9 years ago
sxzhuxu ▴ 50

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 • 1.8k views
ADD COMMENT

Login before adding your answer.

Traffic: 1909 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6