vcf filter of lowQual

Question

[genomics Newbie]

How do I filter my vcf so that all "lowQual" entries are excluded from the variant file.

When I ran the following command I included the -e flag which I thought would exclude all LowQual, but they appear in my vcf and I need to remove them so that I can use my vcf as further input into another pipeline package.

bcftools mpileup -Ou -f /path/to/ucsc.hg19.fasta example.exome.bam | \
    bcftools call -Ou -mv | \
    bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > var.flt.vcf

It did not appear that I can use vcftools to only include "Passed" in the vcf file.

Thank you.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Answer 1

[Kevin Blighe]

To only include those with PASS set in the FILTER column, use:

bcftools view -f PASS

Kevin