Force build conversion?

[teepean]

Hello!

I have received a 23andme formatted file that is in GRCh38 but detects as GRCh37. Is there any way to force the conversion or possibly use more positions to detect the build?

Thanks!

[apriha]

Hello and thanks for the issue! Yes, if you could provide an RSID or two from the file, the detection could add those.

[teepean]

The root cause was that the file was created from a GRCh38 CRAM with WGSExtract and the 23andme header still has mentions of build 37.

[apriha]

Hmm, maybe there could be an option to detect the build using only RSID positions, instead of using them only when the build isn’t in the header.

[teepean]

I think WGSExtract needs to be fixed to create a compatible header depending on the build.

[apriha]

In terms of snps, build detection could be made more robust to just use the data (RSID positions) first, and then fall back to the headers.

[teepean]

To be honest that would be the best solution.