Is there a way to make phased variant calls with samtools/bcftools?

[davidyuyuan]

I built a tool chain to made variant calls against GRCh38. The VCFs are always unphased. I was unable to figure out how to make the variant phased with just samtools & bcftools. Is it feasible or I need to use other tools?

1. samtools phase to create phased bams
2. bcftools mpileup with 2 phased bams as input, then bcftools call --ploidy GRCh38
3. bcftools norm -m +any
4. bcftools filter...

What did I miss? Have I done something wrong?

[pd3]

Currently we have no tool to phase variants within bcftools and samtools phase is largely unsupported. Maybe you'd like to try WhatsHap
https://www.biorxiv.org/content/10.1101/085050v2
https://github.com/whatshap/whatshap

[davidyuyuan]

Thanks, Petr. I was hoping not to drag in Whatshap or other tools. Also, I came across this review by PacBio comparing their own HiPhase with Whathap: https://github.com/PacificBiosciences/HiPhase/blob/main/docs/performance.md in April 2022. Both tools are updated regularly. I would need to compare them side-by-side myself and pick one then.