Extracting VCF information to use in LiftOver

Question

[cookersjs]

Good day,

I am interested in using UCSC's LiftOver tool to convert from GRCh37 to 38. Since VCF's only have the single position in the file, is there any reason I couldn't use the position as both the start and end values?

The reason i'm interested in LiftOver particularly, is that they have the file that can be used from the command-line and it's a simple executable.

I briefly looked at NCBI's Remap (no command-line tool?), and Crossmap (don't want to have python as a dependency).

Any suggestions are welcome!

Thanks

Answer 1

[Pierre Lindenbaum]

Since VCF's only have the single position in the file, is there any reason I couldn't use the position as both the start and end values?

UCSC uses a semi-open (0-based) interval (Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems) using the same start/end (1 based) means you're trying to submit a deletion = 0 bases.

Try to submit:

(variant.chrom):(variant.start-1)-(variant.start)

or use something like LiftoverVcf https://broadinstitute.github.io/picard/command-line-overview.html#LiftoverVcf

[cookersjs]

Thanks very much, I'll make sure to do that!