Lets say I have (dumb example)
CHROM POS REF ALT 1 1 A T
Say this site is hg19 and Ref allele is referring the forward strand and maps to position 100 on hg38.
You can just blindly update the position like this correct?
CHROM POS REF ALT 1 100 A T
I am thinking you cant do this because
- The strand might be different (do strands flip between builds?). If so you would have to report the complement of these nucleotides.
- The nucleotide at that position might have actually been changed (I would think less likely than #1.
Does this seem right?