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:

1. Challenging Medically Relevant Genes small variant and SV benchmarks in HG002
2. Small variant benchmark (v4.2.1) including more difficult regions for all GIAB samples
3. precisionFDA Truth Challenge V2 Manuscript (based on v4.2.1 small variant benchmark) 
4. Collaboration with T2T Consortium using GIAB to benchmark variants in challenging genes on new reference
5. 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

 

Webex meeting information

https://nist-secure.webex.com/nist-secure/j.php?MTID=m7a072dd7b6650c1fcdb32d994d1e6690

 

Join by meeting number:

Meeting number (access code): 2764 901 8890

Meeting password: gsMhgGm@375

 

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Join by phone

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Global call-in numbers

 

[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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