Plinkseq Warning - "Incompatible REF sequences"

[Sugi Sivalingam]

Hi All,

i have a question about a plinkseq warning e.g. "plinkseq warning:  **serious** incompatible REF sequences  : chr1:4".

This is what i observe when I want to read in Plink data and write them out to a VCF file. However I was wondering whether

I can get rid of the reference inconsistencies and filter variant genotypes when a mismatch with the reference allele occur?

Code

./pseq   gsa_array   new-project   --resources /genetics/data/pseq/hg19/   --check-reference

./pseq   gsa_array   load-plink   --file ./gsa_array  --id gsa_array   --check-reference

./pseq   gsa_array   write-vcf   >   gsa_array.vcf

Great would be to have a list of reference mismatches to subset the genotype of interest for these reference misamtches.

Or that they are filtered out before hand so that a VCF from the Plink data can be generated without any incompatible reference

sequences.

Appreciate your help very much.

Thanks and Best