how to enable phasing of final outputs clairTumorOnly

[sahuno]

i see option to phase intermediate vcf and bams plus option todisable_intermediate_phasing . is there anyway to enable phasing of final outputs ? i don't see it.
is there deliberate reason?
thanks in advance!

[JasonCLEI]

Hi @sahuno,

We phase intermediate vcf and haplotag tumor bam for ClairS-TO's haplotype filtering post-processing step, which helps to filter noise signals originates from violating the haplotype assumption. We do not suggest using phasing of final outputs in ClairS-TO's somatic variant calling. Anyway, you can try using WhatsHap or Longphase for phasing attempts.

Regards,
Lei

[sahuno]

Hi @JasonCLEI
Is there any reason (biology/technical) why ClairS-TO doesn't support phasing of final snps? just want to make sure i'm not doing anythiing blindly when i phase ClairS-TO output with WhatsHap or Longphase.

[JasonCLEI]

Hi @sahuno,

We do not suggest using phasing of final outputs in ClairS-TO's somatic variant calling because reliable phasing relies on germline heterozygous SNPs, which are not explicitly indicated in ClairS-TO's final output.

Regards,
Lei