Does anyone know the definitions of the fields that vcftools vcf-stats returns:
- hom_AA = ?
- het_RA =?
- snp_count = total count SNPs
- count = SNP+missing+Ref?
- hom_RR_count = ?
- ref = reference calls?
- missing = missing calls
- private = private calls not found in other samples
- het_AA_count = ?
- ref_count = ? reference calls (same as ref?)
- unphased = unphased snps
The AA, RA and RR confuse me. I thought they might stand for reference and alternative but why is there a hom_RR count, het_AA_count, ref and ref_count field?
Or does anyone know another tools that also provides the total SNP counts per strains and the private SNP counts per strain?