Dear all,
I wish to use mpileup2snp to call SNPs. I am confused by two of the parameters
--min-var-freq NUM A decimal value indicating the minimum VAF for calling variants. For individual samples, 0.20 to allow for variant under-representation. Lower for pooled samples (maybe ½ the expected frequency of a single heterozygote for the most sensitive detection).
--min-freq-for-hom Minimum VAF above which a variant will be called homozygous in a given sample. The default (0.75) is fairly conservative, but addresses the fact that NGS alignments bias toward the reference allele.
If --min-var-freq 0.2 and --min-freq-for-hom 0.75 If Ref=T Alt=A and an individual has 16 reads supporting T and 4 reads support A is this a homozygote or a heterozygote? Ie T has a freq of 0.8 and A has a frequency of 0.2. Therefore, both thresholds are passed? Or does --min-freq-for-hom just refer to the alternative allele?
Why "min-freq-for-hom" is not defined as 1 - "min-var-freq", is there a reason to define different parameters for REF or ALT alleles?
