⚠️ NOTE ⚠️ This article describes behavior present in GATK versions 4.2.3.0 through 4.5.0.0, and is obsolete as of GATK 4.6.0.0, which (by overwhelming popular demand!) reverted back to the standar...
I am fully in line with the authors. The raw all-sites gVCF is the best material to share and should become the gold standard in genomics to move towards standardized and unbiased π estimates. In addition, more metadata regarding the samples and softwares used is needed, including the versions.
Thibault (Tibo) Leroy
Brault et al. propose guidelines for standardized π estimation, systematic reporting of summary statistics, and the adoption of richer metadata to ensure that population genomic data remain comparable and reusable across a wide range of systems.
🔗 doi.org/10.1093/gbe/...
#genome #evolution
