SNPs calling

[zhengluo-zz]

When I use ANGSD for genotype calling, if I perform the calling on a single individual, there are no 0/0 SNPs. However, when calling genotypes for a group together, 0/0 SNPs appear. What could be the reason for this?

[alexpiper]

If you are calling SNPs for a single sample there shouldnt be any 0/0 genotypes, as these are monomorphic reference alleles (i.e. are not Single Nucleotide polymorphisms).

When you are joint calling multiple samples, 0/0 alleles should appear in some samples only when there is a SNP variant (i.e. 0/1, 1/1) at the same position in another sample. Positions with all samples 0/0 shouldnt ever happen in SNP calling.

If you want to keep all monomorphic 0/0 variants you can set -SNP_pval 1.0 to retain all sites.