I followed the samtools/bcfutils/vcfutils pathway followed here http://ged.msu.edu/angus/tutorials-2012/snp_tutorial.html to convert a set of human Hg19-aligned BAM files into a set of raw VCF files. I then got vcftools to filter down to just autosomal SNPs. These are really, really, really low-coverage genomes (they were enriched for NRY and/or mtDNA, and I am just trying to make use of the "leftovers")
Now I have the data I want, but I am trying to found out what of it is actually useable. I was wondering what are good filtering parameters for tossing/keeping human SNPs (or where can I find said parameters)? Thanks!