Double Alleles in gVCF file for ChrX, ChrY & ChrM

Question

[Moe]

Hello, I understand for that for men X,Y, mitochondria chromosomes should be represented by a single allele. but I have a gVCF file that has 2 alleles (homozygous or heterozygous) for each position under these chromosomes, mostly with GT: 0/0, but i also found GT: 0/1 and 1/1. can someone explain?

the reason i'm asking about this is that i'm trying to convert the format from VCF to a TSV format compatible with 23andme.

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  2302-A2767-EXT2
chrM    2   .   A   <NON_REF>   .   .   .   GT:AD:DP:GQ:PL  0/0:108,2:110:99:0,120,1800

chrX    2700027 rs2306736   T   C   1279.03 PASS    AC=2;AF=1;AN=2;DB;DP=45;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;POSITIVE_TRAIN_SITE;QD=28.42;SOR=0.829;VQSLOD=18.15;culprit=QD  GT:AD:DP:GQ:PL  1/1:0,45:45:99:1293,135,0

Thanks

Answer 1

[Pierre Lindenbaum]

POSITIVE_TRAIN_SITE

this VCF looks like it was generated with GATK, and the default parameters GATK are not aware of the ploidy.

https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller#--sample-ploidy

[Moe]

in this case it's easy to just select one allele in case of 0/0 or 1/1 (homozygous) but what if GT: 0/1 (heterozygous), which allele will be the right one?

[Pierre Lindenbaum]

There is no good answer to that question. Depends of the gender, the PAR region, the AD ratio, etc...