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Benchmark hg38: WGS #190

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Madelinehazel opened this issue Jan 22, 2024 · 0 comments
Open

Benchmark hg38: WGS #190

Madelinehazel opened this issue Jan 22, 2024 · 0 comments
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@Madelinehazel
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Madelinehazel commented Jan 22, 2024

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.

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