I've been working on Galaxy to run samtools mpileup function. When I use the supplied reference genome (in my case, mouse mm10), everything runs smoothly and the output bcf works great from my downstream applications.
However, when I try to run the mpileup with a reference genome I provide, I get a bcf that seems to be the appropriate size, but when I convert it to a vcf, I only get the header. I am not sure if I am messing up something with the bcf-->vcf conversion (it works fine with my other samples) or if it is something with me supplying my own reference.
My reference is recognized by Galaxy from my history (it is a .fa). I also added an index file for the reference to my history in case that magically changed something. I have also used my supplied reference for other applications and it worked fine.
If anyone has any suggestions, I would really appreciated them!