GIAB updates and resuming monthly calls
Zook, Justin M. (Fed)
Dear GIAB,
We’re excited to resume GIAB calls every 4 weeks starting Monday, December 12 at 1pm ET. Over the coming months, we plan to discuss several ongoing and new efforts in GIAB, including our draft assembly-based chromosome X+Y benchmark, new methods to model variant calling errors, tandem repeat and SV benchmarks, tumor/normal samples for somatic benchmarks, transcriptomics data, and other topics. I’ve attached a calendar invite, and call-in information is also below. If you have additional suggestions for topics, please let me know!
Also, in case you haven’t seen these, I wanted to link to a number of GIAB-related papers, and you can always find links to the latest GIAB resources at https://www.nist.gov/programs-projects/genome-bottle:
- Challenging Medically Relevant Genes small variant and SV benchmarks in HG002
- Small variant benchmark (v4.2.1) including more difficult regions for all GIAB samples
- precisionFDA Truth Challenge V2 Manuscript (based on v4.2.1 small variant benchmark)
- Collaboration with T2T Consortium using GIAB to benchmark variants in challenging genes on new reference
- Collaboration with Human Pangenome Reference Consortium developing a high-quality diploid assembly of HG002 and using GIAB benchmarks to evaluate assembly-based variant calls
Thanks for all your support of GIAB, and we look forward to seeing many of you on our upcoming calls!
Justin
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Zook, Justin M. (Fed)
Dear GIAB,
Just a reminder that we’ll be having a GIAB call Monday at 1pm ET. A calendar invite is attached if you’d like to add it to your calendar, and more information is in the email below.
Thanks!
Justin
Zook, Justin M. (Fed)
Dear GIAB,
Thanks to all who participated in our call today. If you weren’t able to attend, below are links to a recording and the slides we presented:
https://drive.google.com/file/d/1IhJmHufHCvhdVEgr0yl5YKJXDxWWxb02/view?usp=sharing
https://docs.google.com/presentation/d/1ydraLOFoDihR4lsDTOV4tWxCSp6Oh9oGicvJus92nH4/edit?usp=sharing
We’ll be following up with a call for volunteers to help us evaluate our draft chrX/Y benchmark for HG002 on GRCh38, so stay tuned if you have a high-quality chrX/Y callset you might want to contribute.
Our next call is planned for 4 weeks from now at 1pm ET on Jan 9, where we plan to discuss using an interpretable machine learning model on benchmarking results to help understand how repetitive sequences lead to sequencing and variant call errors.
We hope you enjoy your holidays, and see you in the new year!
Justin
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Zook, Justin M. (Fed)
Dear GIAB analysis team,
We are looking forward to seeing many of you on our GIAB call at 1pm ET today. Nate Dwarshuis from our NIST GIAB team will be presenting his work using GIAB benchmarks with an interpretable machine learning model to predict variant calling errors. If you’re interested in the details, we have a draft manuscript about this work, and we’d welcome your feedback in the next couple days in this google doc: https://docs.google.com/document/d/1qRWfJMv1dG9qfh08SXwSmKVK2qW9RNe9HKP4Hvl80IM/edit?usp=sharing
Thanks!
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Zook, Justin M. (Fed)
Dear GIAB analysis team,
We are looking forward to seeing many of you on our GIAB call at 1pm ET on March 6. Adam English will present about work towards a benchmark set and benchmarking tools specifically for tandem repeats. Look forward to seeing many of you there!
Also, we have done some initial collaborative evaluations of the draft X/Y benchmark we’d presented in December, and it is looking promising. Please email me if any of you would like to participate in the final evaluation by contributing a high-quality callset for HG002’s X and Y chromosomes on GRCh38, and then curating ~75 putative false positives and false negatives we’d send you. For more information, see the recording and the slides we presented in December at:
https://drive.google.com/file/d/1IhJmHufHCvhdVEgr0yl5YKJXDxWWxb02/view?usp=sharing
https://docs.google.com/presentation/d/1ydraLOFoDihR4lsDTOV4tWxCSp6Oh9oGicvJus92nH4/edit?usp=sharing
Zook, Justin M. (Fed)
Dear GIAB Analysis Team,
Just a reminding that we will have our GIAB call today at 1pm ET. Adam English will present about work towards a benchmark set and benchmarking tools specifically for tandem repeats. Look forward to seeing many of you there!
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Cheers,
Justin
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Zook, Justin M. (Fed)
Dear GIAB Analysis Team,
A big thank you to Adam English for a great presentation yesterday about work towards a GIAB benchmark for tandem repeats. His slides are public at https://github.com/ACEnglish/adotto/blob/main/slides/GIAB_Tandem_Repeat_Benchmark_Q12023.pdf if you’d like to review them or missed the call.
Our next call will be April 10 at 1pm ET, one week later than scheduled, and we’ll hear about some initial work understanding sources of variant call errors in tumor/normal cell lines, laying a foundation for future GIAB benchmarks.
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Zook, Justin M. (Fed)
Dear GIAB Analysis Team,
Just a reminder that we moved our regularly scheduled call from April 3 to April 10 at 1pm EDT, and we’ll hear about some initial work understanding sources of variant call errors in tumor/normal cell lines, laying a foundation for future GIAB benchmarks.
Zook, Justin M. (Fed)
Dear GIAB Analysis Team,
We will have our GIAB call today at 1pm EDT. Gail Rosen will present about some initial work understanding sources of variant call errors in tumor/normal cell lines, laying a foundation for future GIAB benchmarks. Look forward to seeing many of you there!
To view this discussion on the web visit https://groups.google.com/d/msgid/giab-analysis-team/PH0PR09MB7931F81D3165E5A8D9EDE7928A8F9%40PH0PR09MB7931.namprd09.prod.outlook.com.
Zook, Justin M. (Fed)
Dear GIAB Analysis Team,
We will have our GIAB call Monday, May 1 at 1pm EDT. We’ll give a brief update on our tumor/normal work, and Tim Dunn will present about his new variant comparison tool vcfdist, which resolves some issues with comparing complex variants (https://www.biorxiv.org/content/10.1101/2023.03.10.532078v2). Look forward to seeing many of you there!
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Cheers,
Justin
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Zook, Justin M. (Fed)
Dear GIAB analysis team,
Since our next GIAB call lands on a US holiday, we are moving it back one week to 1pm ET on June 5. Pete Audano from Christine Beck’s lab will present about his assembly-based variant caller PAV https://github.com/EichlerLab/pav, and how it can be used to call and merge complex SVs, including some new work on CNVs. Look forward to seeing many of you there!
Cheers,
Justin
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Zook, Justin M. (Fed)
Dear GIAB analysis team,
A reminder that we have our GIAB call today at 1pm EDT. I’ll give a brief update on tumor/normal sequencing plans, and Pete Audano from Christine Beck’s lab will present about his assembly-based variant caller PAV https://github.com/EichlerLab/pav, and how it can be used to call and merge complex SVs, including some new work on CNVs. Look forward to seeing many of you there!
Cheers,
Justin
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From: 'Zook, Justin M. (Fed)' via GIAB Analysis Team <giab-anal...@googlegroups.com>
Date: Monday, May 15, 2023 at 4:39 PM
To: GIAB Analysis Team <giab-anal...@googlegroups.com>
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