Benchmark hg38: WGS

[Madelinehazel]

You will run the hg38 crg2 WGS pipeline on NA12878/HG001 from the HapMap project See GIAB for more details, and for links to the benchmark VCF files. For benchmarking instructions, see the Benchmarking section in the crg2 README.

Note: the benchmark rule currently compares to release NISTv3.3.2; please download the files for NISTv4.2.1 and use these instead, and modify the benchmark_hpf.tsv file in the crg2 repo accordingly.

Please also look into benchmarking against trios of Ashkenazi Jewish and Han Chinese ancestry from the Personal Genome Project; GIAB also provides benchmark variant sets for these individuals.

NOTE that you will need to be in branch crg2-hg38, not master, to run the hg38 crg2 pipeline! And for cre, switch to branch hg38 for report generation.