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broadinstitute / gnomad_methods

Hail helper functions for the gnomAD project and Translational Genomics Group
https://gnomad.broadinstitute.org
MIT License
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Meet with Talkowski Group Member / Others about LD Code #723

Closed matren395 closed 3 months ago

matren395 commented 3 months ago

Linkage Disequilibrium code has other stakeholders! I have a meeting planned The Tuesday after Labor Day with a Graduate Student in the Talkowski Lab to discuss some headway that he's made on LD code between SVs and SNVs already! Notes going in this ticket

matren395 commented 3 months ago

Talked about! via slack on 08-27:

so! chatted with our Talkwoski lab friend Daniel Ben-Isvy (another Daniel working on LD code :exploding_head: ) about where his group is at, and they said that their code (actually owned by a one Chris Wheeler) is done (!) for SNV/Indel <-> SV analyses for v3/v4 genomes . It lives as a notebook in Terra , and they’re already using it for some analyses and figures. They’re uninterested in SNVs/Indels . But this raises some questions: for gnomAD v2, we produced and shared a few formats of LD Scores on our v2 Downloads page, and the code for this is in the v2 LD code (wow). These are the outputs that our Talkowksi friends have produced for SNV/Indels<->SVs for v3/v4 genomes , and that I’m not having too much trouble getting working for v3/v4 genome SNPs/Indels (minor troubleshooting pending) Q: Would we want to also share their outputs (SNV<->SV), and if so, Q2: should we host and productionize their code in gnomad_qc ??