Novel Snps-Dbsnp-Contigs
I am working on non-model organism, I have predicted SNPs for each contigs (not chromosomes)and I have output in VCF format. Now I want to find novel SNPs by filtering from dbSNP. I have tried SNPsift which requires VCF input file in chromosome format. Do you know the way to annotate and filter SNPs from dbSNPs for contigs?
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jackuser1979
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if it's a non-model organism, how is present in dbSNP?
Are you using a finished reference or is it a draft assembly? I assume if the organism has a dbSNP it should likely have a finished reference that you can use for variant calling.