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6.9 years ago
Ann
•
0
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!
