Empty VCF

[vymao]

Hi,

I tried running Strelka, and while there seems to be no error (in any of the logs), there are no calls in the variant VCF. There is a VCF header, but no calls of any kind. This issue seems to have been raised before but not addressed; is there a reason for this?

[N-TI]

Hi,

I have the same the problem as you. Did you find a reason of this problem? First time I run strelka, I got a data however when I wanted to run it again on the same data (and other data), I got empty VCFs without error message.

Thank you

[Gaodelike]

I also encountered the same problem. I don't know if it is the reason for mapping. Do you know what the reason is?

[Giuseppe1995]

Hi, I've also encountered the same issue, and (in my case) the problem was that some samples had 0 properly paired reads (samtools flagstat output). you can find a tread about it here. However, always in my case, the problem stood in the phase of reads trimming (I used fastp). Skipping this step allowed me to solve the problem (luckily the percentage of trimmed reads was so low that probably these samples had been trimmed before, so no problem skipping trimming procedure) and call variants with Strelka correctly.