Hello,

I'm trying to filter the good quality SNPs on a vcf file using the below command:

vcfutils.pl varFilter –p –Q50 –d5 –a3 sample1_mpileup.unfilt2.vcf > filtered.vcf

The filtered.vcf files doesn't have any PASS marks in the filter column. There is just a dot. The filtered.vcf file also seems to have random lines/SNPs removed from the file i.e. there doesn't seem to be a pattern as to the type of SNP that has been removed.

If anyone has any advice that would be great!

Thanks!