Haplotype filtering step keep stuck

[hku-bal]

Haplotype filtering step keep stuck

[zhengzhenxian]

Hi,

Based on the information provided, the issue is possibly due to a zombie process caused by multi-processing in the haplotype filtering submodule.

We tried to rewrite the function and test locally, please try to re-pull the docker image (You might need to remove your local image first using dcoker rmi hkubal/clairs:latest ). If the issue persists, pls kindly let us know, thanks!

Zhenxian

[tahashmi]

Thanks!
I will try and let you know.

[tahashmi]

This fix works. Thanks.
With --phase_tumor True, in which directory should I expect single (combined) phased tumor VCF and single haplotagged BAM?

[zhengzhenxian]

Hi,

The phasable somatic variants are tagged with H in the INFO column already. You could find the haplotagged BAM in ${OUTPUT_DIR}/tmp/clair3_output/phased_output/ directory, but pls note that the BAM were haplotagged using the called germline variants in tumor and normal sample.