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lawremi / rtracklayer

R interface to genome annotation files and the UCSC genome browser
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Liftover convert hg38 to hg19 #107

Closed JingjingBai2021 closed 10 months ago

JingjingBai2021 commented 10 months ago

Hi, I am trying to convert a list of snps from hg38 to hg19.

Most of the snps have converted sucessfully with the same position in dbSNP. But some SNPs' positions are off 1.

Unconverted SNP: rs1385708574 BP: 98999310 Liftover converted: rs1385708574 BP:99651564 dbSNP: rs1385708574 BP:99651565

How to fix these? I converted data frame to GRanges object to lift the coordinates. SNP start and end were labeled the same. Best, Jingjing

lawremi commented 10 months ago

This is likely due to the imprecise nature of the lift over. This question is better suited for support.bioconductor.org. It's not clear (yet) that this is an issue with the package itself.