no variants - wgs data

[StephanHolgerD]

Hello, I tried to run strelka on a wgs dataset with matched tumor and normal tissue, i also fed in the smallindels file from manta but unfortunately the result vcf files are all empty. The header of the .vcf files is correct but herea are not variants reported. But as far as I see there are no errors in the log files.

[vymao]

Hi Stephan, I am getting the same error. Did you figure this out?

[StephanHolgerD]

I remapped my data using bwa-mem afterwards everything worked out fine for me

[Gaodelike]

之后我使用 bwa-mem 重新映射了我的数据，一切对我来说都很好

After remapped, do you need to sort and tag the repeat sequence again for the bamfile?

[sagitaninta]

Just wanna add to this discussion for future people that stumbled on the same problem: I experienced the same thing after filtering my BAM file and the working solution is to sort the filtered BAM first before running strelka. It works for me.