the output of vcf-stats like this:
I don't understand the means of "ref homs, nonref homs, ref hets, nonref hets". According to my understand, for one site, the reference genotype is "A"
ref homs: A (ref), A (sample)
nonref homs: A (ref), G (sample)
ref hets: A (ref), A/T (sample)
nonref hets: A (ref), T/C (sample)
Is it right?
Thank you!
Code:
Rows with a call 3264597 SNP alleles 2594406 indel alleles 618033 other events 0 ref homs 1107825 (33.9%) nonref homs 1055574 (32.3%) ref hets 1101105 (33.7%) nonref hets 0 (0.0%)
ref homs: A (ref), A (sample)
nonref homs: A (ref), G (sample)
ref hets: A (ref), A/T (sample)
nonref hets: A (ref), T/C (sample)
Is it right?
Thank you!