Table 3 Clair3 training and evaluation pipelines
From: nPoRe: n-polymer realigner for improved pileup-based variant calling
Step | clair3 | clair3-hap | clair3-npore-hap | Program |
|---|---|---|---|---|
Align reads | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | minimap2 |
Generate tensors | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | clair3/CTP.py |
Train clair3 | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | clair3/Train.py |
Call variants | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | clair3/run_clair3.sh |
Phase variants | \(\checkmark\) | \(\checkmark\) | whatshap phase | |
Phase reads | \(\checkmark\) | \(\checkmark\) | whatshap haplotag | |
Phase truth VCF | \(\checkmark\) | \(\checkmark\) | whatshap phase | |
Standardize truth VCF | \(\checkmark\) | nPoRe/standardize_vcf.py | ||
Realign reads | \(\checkmark\) | nPoRe/realign.py | ||
Generate haplotype tensors | \(\checkmark\) | \(\checkmark\) | clair3-hap/CTPHaps.py | |
Train model | \(\checkmark\) | \(\checkmark\) | clair3-hap/Train.py | |
Call variants | \(\checkmark\) | \(\checkmark\) | clair3-hap/run_clair3.sh | |
Evaluate variants | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | hap.py |