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validate variant calls with seqc2 consortium data #33

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kelly-sovacool opened this issue Feb 9, 2024 · 0 comments

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kelly-sovacool commented Feb 9, 2024 •

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seqc paper

raw data https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/data/
high confidence variant calls https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/

we could subsample to 1 chromosome for a small test dataset for development

nf-core/sarek uses seqc2 for benchmarking

hap.py

use to benchmark against high confidence data https://hpc.nih.gov/apps/hap.py.html

kelly-sovacool changed the title ~~validate variant calls with seqc~~ validate variant calls with seqc2 consortium data

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