phased VCF output?

[RichardCorbett]

Hi folks,

I'm finding the tool works really well and much better than other tools. I have a question about where to find the phased variants in the output. I can see that whatshap is run on my human sample and there are many split-by-chromosome files in /tmp/phase_output/phase_bam and /tmp/phase_output/phase_vcf. However, my final merge_output.vcf.gz doesn't appear to contain any phased variants.

I am running a GM24385 30X bam file with the following command:

/opt/bin/run_clair3.sh 		--bam_fn=PAH62362_pass.bam 		--ref_fn=hg38_no_alt_TCGA_HTMCP_HPVs.fa 		--threads=48 		--platform="ont" 		--model_path="/opt/models/ont" 		--output=clair_3_0_1_F79937 		--whatshap=/opt/conda/envs/clair3/bin/whatshap 		--include_all_ctgs

Where should I be looking for the final phased results?

thanks
Richard

[aquaskyline]

Clair3 doesn't provide phased variant output. But we have received many requests in the past months for providing phased variant output. Thus we are preparing a new release (release 8) that allows users to use whatshap to phase the variant calls for output. We will release the new version late this week, stay tuned.

[aquaskyline]

Phased VCF output provided in v0.1-r8.

[RichardCorbett]

Thanks! Testing it out and it seems to work as expected.