New HG003 and HG004 benchmarks and GIAB call on Monday, July 13
Zook, Justin M. (Fed)
Dear GIAB Analysis Team,
We are excited to release a draft v4.2 benchmark developed from short, linked, and long reads for the entire Ashkenazi trio (HG002, HG003, and HG004). We’d greatly appreciate any feedback about this new version, available under:
As described in the README, the main changes in v4.2 from v4.1 are:
1. We now use hifiasm to perform the assembly of PacBio HiFi reads in the MHC, and use dipcall with this assembly to call variants, including in segmental duplications that were previously not assembled properly. Since it represents complex variants as individual SNVs and indels, dipcall helps improve partial credit in some cases for variants that are only partially called correctly by the query callset. We also now exclude entire homopolymers and tandem repeats in the MHC if they are not completely covered by the benchmark bed. For HG003 and HG004, the MHC was not fully phased or assembled in a single contig for each haplotype, but the regions around breaks in the contigs are excluded from the benchmark regions.
2. Since calls are made for HG003 and HG004 in addition to HG002, we now perform a trio Mendelian analysis and exclude most Mendelian violations from the benchmark regions for all individuals. An exception is that putative de novo variants in HG002 are not excluded from the benchmark regions.
We’ll be having a GIAB Analysis Team call on Monday, July 13, at 3pm EDT, to talk about this new benchmark, talk about submission plans, and receive any final suggestions on the draft manuscript at https://docs.google.com/document/d/12xTVZCftW2pPgqtWr9QchiFABWzhW4-3A5sWR_5mt_s/edit?usp=sharing
Note this new connection information:
https://bluejeans.com/504191468
(Join from computer or phone)
Phone Dial-in
+1.408.317.9254 (US (San Jose))
+1.408.740.7256 (US (San Jose))
(Global Numbers)
Meeting ID: 504 191 468
Room System
199.48.152.152 or bjn.vc
Meeting ID: 504 191 468
Cheers,
Justin
Zook, Justin M. (Fed)
Dear GIAB Analysis Team,
A reminder that we’ll be having our call this afternoon at 3pm EDT about the new v4.2 benchmarks and paper with the new bluejeans connection information below.
Cheers,
Justin
Zook, Justin M. (Fed)
Hi all,
I’ve attached the updated slides Justin Wagner and I presented on the call Monday, including an outline of ongoing and future work on the last slide. We are currently working on finalizing the manuscript about the v4 small variant benchmark at the link below, and we plan to submit to biorxiv and likely to Nature Biotechnology next week, so now is a great time to make any final suggestions before the manuscript is submitted.
https://docs.google.com/document/d/12xTVZCftW2pPgqtWr9QchiFABWzhW4-3A5sWR_5mt_s/edit?usp=sharing
Thank you for all your contributions!
Zook, Justin M. (Fed)
Hi GIAB Team,
Just a quick update that our manuscript about the new small variant benchmark is now submitted to biorxiv and to Nature Biotechnology. Thank you all for your contributions to this manuscript, and we’ll let you know when we have the link for biorxiv! We won’t have the call on Monday, and plan to have our next GIAB analysis team call August 10.
Cheers,
Justin
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