Fix hg38 -> hg19 liftover

[GFJHogue]

It looks like the liftover logic was actually changed and broken at some point after Wei's original/website code - and unfortunately that made its way into the working copy used to start this repo.

Anyhow, the liftover process wasn't properly handling reverse-stranded lifts, thereby causing a systemic -2 coordinate error, and more concerningly yielding incorrect bases in these cases.

I've fixed this to the best of my knowledge and added more informative Liftover warning stderr logs to help diagnose any related issues going forward.
These warnings are expected in cases where a base may have been changed between hg19 and hg38 - in these situations the ALT most often matches the hg19 reference.

[lstein]

We need a set of tumour VCFs with known correct results to use as regression tests. This can't keep happening! Lincoln

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On Fri, Aug 29, 2025 at 5:46 PM Greg Hogue ***@***.***> wrote: It looks like the liftover logic was actually changed and broken at some point after Wei's original/website code - and unfortunately that made its way into the working copy used to start this repo. Anyhow, the liftover process wasn't properly handling reverse-stranded lifts, thereby causing a systemic -2 coordinate error, and more concerningly yielding incorrect bases in these cases. I've fixed this to the best of my knowledge and added more informative Liftover warning stderr logs to help diagnose any related issues going forward. These warnings are expected in cases where a base may have been changed between hg19 and hg38 - in these situations the ALT most often matches the hg19 reference. ------------------------------ You can view, comment on, or merge this pull request online at: #5 Commit Summary - 0c357c8 <0c357c8> fix vcf liftover File Changes (1 file <https://github.com/LincolnSteinLab/DeepTumour/pull/5/files>) - *M* src/utils.py <https://github.com/LincolnSteinLab/DeepTumour/pull/5/files#diff-51246e53255db77c9edad496f074aa1bdbf8dbdc11f89a02040115c9ab4fa7f0> (39) Patch Links: - https://github.com/LincolnSteinLab/DeepTumour/pull/5.patch - https://github.com/LincolnSteinLab/DeepTumour/pull/5.diff — Reply to this email directly, view it on GitHub <#5>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAA3EVKDFAKBTWWNNEBAQ4D3QDC3FAVCNFSM6AAAAACFFVGNOCVHI2DSMVQWIX3LMV43ASLTON2WKOZTGM3DQMRYGI3DONY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Lincoln Stein (he/him/his) Scientific Director (Acting), and Head, Adaptive Oncology Ontario Institute for Cancer Research Faculty Affiliate, Vector Institute Professor, Molecular Genetics, University of Toronto ***@***.*** Tel: 416-673-8514 | Cell: 416-817-8240 Executive Assistant Michelle Xin ***@***.*** Tel: 647-260-7927 Ontario Institute for Cancer Research MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca Collaborate. Translate. Change lives. This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

[GFJHogue]

Oh, there it is LincolnSteinLab/oncoGAN@f20736f#diff-2845ef4c7e134a3f3e162b1661a4fe9bc019bb4287e701186379631ce03b32cbR15