This directory contains v1.0.0 of highly accurate somatic benchmarking single nucleotide variants (SNVs), small indels (indels), structural variations (SVs), and mobile element insertions (MEIs) for the HapMap cell line mixture. The HapMap mixture consists of 83.5% of HG005 (Chinese male), 10% of HG02622 (European/Ashkenazi Jewish male), 2% of HG002 (African female), 2% of HG02257 (African male), 2% of HG02486 (East Asian female), and 0.5% HG00438 (Chinese male). The vcf.gz and bed files are intended to be used together to benchmark the performance of somatic variant callers. The benchmarking region is defined as the intersection of reliable regions across the 12 haploid assemblies from the 6 HapMap samples, encompassing 89% of GRCh38 and 90% of CHM13, respectively. The following paper(s) can be cited for use of the benchmark variant set: TBD.

Files under the current directory:
1. The bed file and gzipped vcf files directly under GRCh38 and CHM13 subfolders are the regions and graph-based somatic variants to use for benchmarking.