Expanded small variant benchmark now available for all GIAB samples!

[Zook, Justin M. (Fed)]

Dear Genome in a Bottle Consortium,

 

We are excited to have completed and release the v4.2.1 small variant benchmark for all 7 GIAB samples on GRCh37 and GRCh38. This benchmark used short, linked, and long reads to include more challenging regions than v3.3.2, such as segmentally duplicated genes like PMS2.  The benchmark vcf and bed files are available under https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/. We’ve included new preliminary phasing for HG001, HG002, and HG005 using phased assemblies under SupplementaryFiles, and we welcome your feedback. We’ve updated the preprint to include all samples, as well as other updates to figures, text, and code, at https://doi.org/10.1101/2020.07.24.212712. We’ve also updated the preprint about our Challenging Medically-Relevant Genes benchmark for HG002 at https://doi.org/10.1101/2021.06.07.444885. We are also close to finalizing a new version of GIAB/GA4GH stratifications with new stratifications from v4.2.1, challenging medically relevant genes, and Telomere to Telomere Consortium work. We are evaluating approaches to develop future assembly-based benchmarks for chromosomes X and Y and for diploid autosomes. We will be sending a new schedule for GIAB analysis team calls to the analysis team list to discuss ongoing work in the near future. Thank you for all of your contributions to this work, and as always, please let us know if you have any suggestions or feedback.

 

Cheers,

Justin, on behalf of the NIST Human Genomics Team