I did detection of SNPs from WG re-sequenced data of 25 pigs(~10x). I found out that many SNPs with flanking sequence hitting twice or thrice in QTL region. I already did primary filtering on SNPs such as remove SNPs within repeats, set min depth of ref and non-ref allele to 2.
Now i need to choose SNP for genotyping purpose. is it important to remove all SNPs with multiple hits?
Welcome any suggestion!!