Liftover handling of *

[ahasuni]

Sorry, this is not an issue, just a question regarding the difference between picard liftover and your tool.

I recently tried picard's liftover for lifting over from 37 to 38, and I came across this issue regarding asterisks (*) in the ref/alt field of my VCFv4.2 file:

#CHROM POS ID REF ALT QUAL
9 10469 . G * .
9 10793 . C * .
9 10976 . C * .

This caused the tool to crash and the only way around it was to delete those rows. Im curious as to how your bcftool pluggin handles these asterisks? Will I have to remove as well? Any suggestions?

[freeseek]

Make sure you are using the latest version of the tool and these variants should liftover like regular SNVs