What is it?
Note that these QC metrics are calculated more for descriptive and informative purposes than for quality control per se. As such they are normally set to values that will never result in a failing sample.
nhet_maxcheck the proportion and absolute number respectively of heterozygous genotype calls in the imputed VCF delivered for a given sample, and check that they are below a given maximum.
nhalt_mincheck the number of homozygous reference and homozygous alternate genotype calls in the imputed VCF delivered for a given sample, and check that they are above a given minimum
Possible reasons for failure:
- Excess heterozygosity (i.e., the presence of a higher number of heterozygous calls in the imputed VCF than the given threshold) would result in these QC metrics failing
- Excess heterozygosity may indicate the presence of sample contamination.