Post date: Sep 30, 2013 12:13:9 AM
I used bcftools view to identify and print variable sites from the bcf file(s). I am unable to generate variable sites from the bcf file made using the -6 option (illumina 1.8+ encoding). This is likely fine as this should be the wrong encoding.
I am identifying variants with two levels of stringency: more stringent (wildwgVarsA.vcf) with -d 0.8, -p 0.001, -P full, and -t 0.001, and less stringent (wildwgVarsB.vcf) with -d 0.2, -p 0.01, -P full, and -t 0.001. Note that because this is whole genome re-sequence data (rather than restriction fragment sequence data) it might be fine to use the less stringent criteria (n particular, it might not be necessary to require most individuals to have data for a variable site).