Debug LiftOver Failures
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2.5 years ago
afollette • 0

I often have to LiftOver genome coordinates for SNV from GRCh37 to GRCh38. Recently, I found a SNV in TP53 that did not LiftOver from 37 to 38 because it is "Deleted in new". The data point is chr17:7578403 C T. Using the UCSC data table I have found that this genomic position is located in an exon. I am assuming this sequence might have been moved to an _ALT allele in GRCh38.

I would like to know what is the easiest way to troubleshoot these LiftOver failures like this. I have tried using UCSC Table Browser to compare tracks, but I have not found tracks that are very informative. Should I look at the GRC contig and it's history or is there another easier way to debug and visualize these LiftOver failures?

LiftOver NCBI Remapping GRCh37 GRCh38 • 613 views

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