Different output

[pcr876]

Hi,

First of all thank you for ClairS-TO.
I have been trying to use it with bed file option.
I get different output for the same sample if I re-run it.
In some output, it skips certain positions of a chromosome. It shows in the tmp file if I check individual chromosome vcf file. But some positions or entire chromosome get missed out in a merged output vcf. Also does not show phasing in a final vcf.

Thank you in advance.

Shreya

[aquaskyline]

can you send us the complete log file.

[pcr876]

I have emailed you the files @aquaskyline