Problem variants?

[smlmbrt]

Some reports:

variants with a valid rsid tags but an "Unknown" source reference tag or “NR” genome_build tag, though it also occurs in some novel variants. For example PGS003753_hmPOS_GRCh38.txt.gz rs147937400 (T>C), which seems to correspond to an original reference of GRCh37 (chr6 29068745), but appears unmapped in the PGS Catalog’s GRCh38 harmonized score file (UCSC reports it mapped to chr6 29100968 in GRCh38)

Related to PGScatalog/pgsc_calc#137

[smlmbrt]

@ens-lgil can we look at which it seems to miss that rsID? It seems 104/35445 don't map and get "Unknown" but at least rs147937400 should be mapped to chr6 via ensembl: https://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=6:29100468-29101468;v=rs147937400;vdb=variation;vf=193308664

[ens-lgil]

Yes, it seems that it's an issue with the UCSC liftover. We need to find an other mapping source when this happens.

[smlmbrt]

But that one should have been mapped by the rsID to chr6, not the liftover.

[ens-lgil]

This PR should fix at least partially the issue: PGScatalog/pgs_variants_coords#4

[smlmbrt]

Will it require re-running everything?

[ens-lgil]

Yes, just to be on the safe side. Or at least each Harmonized files with "Unknown" source + rsID column