strelka error

[eesiribloom]

I am running in to an error similar to these when trying to run impala:
see here
and here

Is this something you were able to troubleshoot ?

[eesiribloom]

I think I have worked out the issue is coming from the fact that in my case the vcf file has contigs which are not specified in the STAR alignment BAM file. I will go back and see if I can fix this

[oneillkza]

Yep that sounds like a likely cause! You may need to regenerate one or the other.