Please define 'wrong ref'. The issue may relate to this: A: Alternate nucleotide is more frequent than reference nucleotide. OMG I'm dizzy.
What i mean is just like this : Chrom Pos Ref Alt 1 1200 A G
But in the published genome fasta file,the chromsome 1 position 1200 nucleotide is T。 So my snp`s ref is not same as the nucleotide in published genome fasta file. How can i extract this kind of snp from my vcf file ?
I see. Please take a look at the --check-ref option in bcftools norm:
-c, --check-ref <e|w|x|s> check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]
You will also have to specify an input FASTA genome, of course.
Log in to answer this question.
