Does anyone know of a program that can call SNPs with low coverage? I have been using samtools mpileup and bcftools/vcftools to find high confident SNPs. I am now trying to identify unknown samples based off of the reference SNP panel I generated. Therefore, I don't need high confidence in calling SNPs in these unknown samples since I know the SNP exists and since I will compare hundreds of these SNPs unknown sample calls. I am dealing with coverage in matters of about 3-5x on average. I really appreciate any suggestions.