validate variant calls with seqc2 consortium data #33
Description
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