New v4.2.1 small variant benchmark and precisionFDA challenge manuscripts

[Zook, Justin M. (Fed)]

Dear Genome in a Bottle Community,

 

We’re excited to make two new resources available for benchmarking small variants in challenging regions of the genome, including in difficult genes like PMS2 and the MHC:

1. We have released the v4.2.1 benchmark for HG002, HG003, and HG004 on both GRCh37 and GRCh38.  This version has a few refinements described in the readme, and is also the first benchmark using long reads for the parents on GRCh37.  A new version of the preprint updated to describe v4.2.1 is at https://doi.org/10.1101/2020.07.24.212712, and the benchmarks are available under the NISTv4.2.1 directory for each genome at. ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/
2. As an important example use case of the v4.2.1 benchmark, we have worked with precisionFDA to post a preprint about the precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions at https://doi.org/10.1101/2020.11.13.380741.

 

Thank you to all of you who contributed to this work, and please let us know if you have any questions or have any suggestions for these resources!

 

Justin