How to remove Variants where the Ref and Alt in the reference genome are switched?

Question

[O.ibra]

I ran the sample twice on a WES platform, and there is about 3% discordance between the 2 VCFs. Most of the discordant "variants" seem to be homozygous Refs in the databases, except that the reference genome has the other allele as Ref. It seems to be a problem with the ref genome (hg19). Is there a way to filter out such variants?

Thanks

Answer 1

[Pierre Lindenbaum]

bcftools norm in https://samtools.github.io/bcftools/bcftools.html

-c, --check-ref e|w|x|s

what to do when incorrect or missing REF allele is encountered: exit (e), warn (w), exclude (x), or set/fix (s) bad sites. The w option can be combined with x and s. Note that s can swap alleles and will update genotypes (GT) and AC counts, but will not attempt to fix PL or other fields.