vcf filter of lowQual
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.
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Kevin Blighe
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genomics Newbie •
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To only include those with PASS set in the FILTER column, use:
bcftools view -f PASS
Kevin
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