Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Fixed a bug when the contig name contains colons (#203)
whatshap haplotag
step is ~15% faster. (#193).--keep_iupac_bases
to keep the IUPAC bases (#153).--use_longphase_for_intermediate_phasing
, --use_whatshap_for_final_output_phasing
, --use_longphase_for_final_output_phasing
, --use_whatshap_for_final_output_haplotagging
to disambiguate intermediate phasing and final VCF phasing either using WhatsHap or LongPhase, old options are still usable (#164).