Lifting over results in coordinates that do not agree with what the rsid suggests the coordinates should be?
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15 months ago
curious ▴ 620

I am trying to sync up bim files from two different builds so that they have the same position and rsid for each variant

I have a bim file A from a respected group that has this line and is on hg18 coordinates

6  rs1755047    0  33478210   C   G

my own bim file B on hg19 has this line, these coordinates agree with what dbsnp reports for this rsid on hg19:

6  rs1755047 0  33431319   C   G

If I use UCSC liftover, the tool says chr6:33431319 on hg19 maps to chr6:33539297 on hg18. I would have expected chr6:33478210 given the info in bim A.

I have 1700 of these I need to snyc up. Out of these only 80 seem to liftover properly, in the sense that lifting over bim file A from hg19 to hg18 leaves me with coordinates and rsids that match up perfectly with bim file B.

This is in the HLA region if that that makes a difference. Pretty stuck here any advice would be greatly appreciated

liftover hla • 404 views
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