domains / families / science / clair3-variants

clair3-variants

separate

Calls germline small variants (SNPs and indels) from Oxford Nanopore and PacBio HiFi long reads with Clair3, a two-stage (pileup + full-alignment) deep-learning caller, selecting the chemistry- and basecaller-version-matched model, enabling read-based phasing, and benchmarking against GIAB with stratification. Covers why the model string is the experiment (no auto-detection, silent degradation on mismatch), why ONT homopolymer/STR indels are the residual error whole-genome F1 hides, and the somatic/trio/RNA boundary to the ClairS/Clair3-Trio family. Use when calling germline SNVs/indels from ONT or HiFi BAMs, choosing a Clair3 model, phasing variants, or benchmarking long-read calls.

When to use

• calling germline SNVs/indels from ONT or HiFi BAMs
• choosing a Clair3 model
• phasing variants
• benchmarking long-read calls
• germline diploid SNPs + small indels
• non-human / draft / bacterial reference calling
• cohort joint genotyping via gVCF

When not to use

• structural variants
• somatic/mosaic variants
• RNA variants
• PacBio CLR data

Skill page

Source