Question: CrossMaps tool failure mapping
0
gravatar for melania 2282
8 weeks ago by
melania 228290
melania 228290 wrote:

Hello, I tried CrossMaps tool to update genotyping data from Grch37 to grch38. But I noticed that for each chromosome at least 30% failed to map, this rate of failutre is it acceptable ?

Thank you very much

snp grch38 grch37 • 106 views
ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by melania 228290
1

If these are loci that changed positions in the more recent assembly then there is nothing you can do about it other than realigning and repeat the variant calling with GRCh38.

ADD REPLYlink written 8 weeks ago by ATpoint40k

Thank you ATpoint, but i think such tool could update the positions accordind to the new assembly ?

ADD REPLYlink written 8 weeks ago by melania 228290
1

If these regions are e.g. not part of the new assembly anymore because it turned out the 37 assembly was flawed at the position and the region got dropped entirely then you cannot update it. Depends on what you want to do with the data but if possible remap and call variants again, far more robust than any liftovers.

ADD REPLYlink written 8 weeks ago by ATpoint40k
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