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Evaluate DV calling on HG001 AKA NA12878 using its new assembly-based benchmark #60

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adamnovak opened this issue Nov 5, 2024 · 2 comments
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@adamnovak
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See https://www.biorxiv.org/content/10.1101/2024.10.02.616333v1

This ought to have been held out.

We want this alongside HG002 assembly-based and HG002 GIAB benchmarks.

@adamnovak adamnovak self-assigned this Nov 5, 2024
@adamnovak
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I found some real HiFi Revio and R10 reads for HG001, and the truth VCF is s3://platinum-pedigree-data/data/variants/small_variant_truthset/GRCh38/CEPH1463.GRCh38.family-truthset.ov.vcf.gz where NA12878 is alongside other samples. But the truth here is on GRCh38 so we can't run HG001 on a CHM13 reference.

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adamnovak commented Jan 7, 2025

I have taught the Snakemake how to get HG001 truth sets from s3://platinum-pedigree-data/variants/assembly-based/dipcall/. That's where the actual assembly-based truth sets are. They are available for both GRCh38 and CHM13.

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