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andrewSharo / StrVCTVRE

StrVCTVRE, a structural variant classifier for exonic deletions and duplications

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Hg19 integration?

mkinnaman opened this issue · comments

commented

Lot of potential with this tool!

WIll you be rolling out a version that works with HG19 genomes?

Thanks,
MIchael

commented

Hi Michael,

Thanks for your interest in StrVCTVRE! I'm happy to include an option for hg19. If you're going to be working with a lot of SV data, I do recommend considering the switch to hg38. It's a better build for SV detection and most major databases now support hg38.

As you're likely already aware, you can also use the UCSC liftover tool (https://genome.ucsc.edu/cgi-bin/hgLiftOver) in the mean time to convert from hg19 to hg38. This will however not work for all SVs, so it's not a perfect solution. I'll reply to this message when I release a hg19 version so you're updated right away.

Best, Andrew

commented

StrVCTVRE can now annotate SVs in hg19/GRCh37 coordinates.