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enormandeau / snplift

Transfer coordinates across genomes
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Orientation of SNPs #6

Closed DuttaAnik closed 10 months ago

DuttaAnik commented 10 months ago

Hello, Thanks again for developing this super useful tool. Along with lifting new SNP positions, would it be possible to add a function to check or update the SNP orientation as well? This will help a lot. Thanks.

enormandeau commented 10 months ago

Could you describe exactly what you mean by updating SNP orientation?

DuttaAnik commented 10 months ago

Hi, so I meant that SNP can be reported in the context of forward or reverse strand based on which strand (forward or reverse) is used as the reference. For example, a C/G SNP on the forward strand is a G/C SNP on the reverse strand due to complementary base pairing. So, I was wondering if the SNPlift tool can provide such strand information after lifting the SNPs.

enormandeau commented 10 months ago

In the config file, by default you have:

export CORRECT_ALLELES=1 # Reverse complement alleles when new genome region is inverted [0, 1].

I think that should do what you want.