Question: Duplicate Snps
gravatar for vibes1002003
7.5 years ago by
vibes100200330 wrote:

Dear all,

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!!

Regards Rahul

snp • 1.5k views
ADD COMMENTlink modified 6.2 years ago by Biostar ♦♦ 20 • written 7.5 years ago by vibes100200330
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