I have vcf files of a single denisovan individual. The file contains information on every position on every chromosome for the individual, not just variants. However, with some variants although the alt field shows a different nucleotide to the ref field, the allele count is still 0, as is the allele frequency, and the genotype is shown as 0/0. Here is an example:
20 122859 rs185918670 T C 111.25 . AC=0;AF=0;AN=2;DP=27;MQ=37;MQ0=0;1000gALT=C;AF1000g=0;RM;TS=HPOMC;CAnc=T;OAnc=T;rMac=T;bSC=955;mSC=0.049;pSC=0.362;Map20=1 GT:DP:GQ:PL:A:C:G:T:IR 0/0:27:81.26:0,81,1047:0,0:0,0:0,0:20,7:0
In an instance like the above should this be regarded as a homozygous locus and the alt allele field be ignored, or am I misreading the information in some way?