Precedence between alt field and GT info in vcf files

Question

[spiral01]

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?

Answer 1

[Gabriel R.]

I assume you are talking about this VCF file:

http://cdna.eva.mpg.de/denisova/VCF/hg19_1000g/T_hg19_1000g.20.mod.vcf.gz

The BAM file at that position contains 20 Ts on the + strand, 7 on the - strand. I am not sure as to why there is an alternative allele but I can tell you that a custom script was used to produce those from an older version of GATK. The reason being is that the older GATK could not call heterozygous for 2 alternatives but we could set the reference bias to 0. The newer GATK could call heterozygous for 2 alternatives but we could not set the reference bias to 0. The solution that what we had to do is: 1) call genotypes once with the older version of GATK on the normal genome, 2) mutilate the reference to add alternative alleles and 3) recall genotypes on this reference, 4) combine both calls into one. There could have been some errors along the way.

[spiral01]

Thanks for your response. The files are actually from here:

http://cdna.eva.mpg.de/neandertal/Vindija/VCF/Denisova/chr20_mq25_mapab100.vcf.gz

Does this mean the alternatives should be ignored and the GT information take precedence?

[Gabriel R.]

But the line you copy pasted was from http://cdna.eva.mpg.de/denisova/VCF/hg19_1000g/T_hg19_1000g.20.mod.vcf.gz right?