Question: How to remove Variants where the Ref and Alt in the reference genome are switched?
0
gravatar for O.ibra
9 months ago by
O.ibra0
O.ibra0 wrote:

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

variantcalling refalt wes ngs • 218 views
ADD COMMENTlink modified 9 months ago by Pierre Lindenbaum119k • written 9 months ago by O.ibra0
0
gravatar for Pierre Lindenbaum
9 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

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.

ADD COMMENTlink written 9 months ago by Pierre Lindenbaum119k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1030 users visited in the last hour