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freeseek / score

Tools to work with GWAS-VCF summary statistics files
MIT License
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Liftover handling of * #21

Open ahasuni opened 1 month ago

ahasuni commented 1 month ago

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 commented 1 month ago

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