validate variant calls with seqc2 consortium data - Githubissues

CCBR / LOGAN

https://ccbr.github.io/LOGAN/

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validate variant calls with seqc2 consortium data #33

Open kelly-sovacool opened 5 months ago

kelly-sovacool commented 5 months ago

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