New papers about GIAB benchmark sets and best practices for benchmarking

[Zook, Justin (Fed)]

Dear Genome in a Bottle,

 

We are excited that two papers describing GIAB and GA4GH work have recently been published in Nature Biotechnology:

 

1. “An open resource for accurately benchmarking small variant and reference calls” describes the improved, reproducible methods used to form the widely used GIAB small variant benchmark set (v3.3.2, released in Feb 2017) for 7 genomes, including 6 broadly-consented genomes from the Personal Genome Project. These methods cover ~90 % of GRCh37 and GRCh38, with 17 % more SNPs and 176 % more indels than our methods published in 2014. https://rdcu.be/bue67  
2. The second describes “Best practices for benchmarking germline small-variant calls in human genomes” using high-confidence calls and regions like those described in the paper above.  The methods developed and standardized by the GA4GH Benchmarking Team enable sophisticated comparison of variant call files, output of standardized performance metrics, and stratification of performance by variant type and genome context. https://rdcu.be/bqpDT

 

We are grateful to many collaborators in GIAB and GA4GH who have made this work possible.  We are excited to continue our work with the GIAB community developing benchmark calls and benchmarking methods for increasingly difficult variants and regions of the genome!

 

Cheers,

Justin and Marc