Hal2Maf for PhastCons

[francicco]

Hi @glennhickey,

I'm trying to run a PhastCons analysis in order to identify conserved elements.
I'm converting each chromosome with the following command:

hal2maf --refGenome $SP --noAncestors --noDupes --onlyOrthologs --refSequence $scf $HAL $scf.maf

I do my phastCons search for rho and then I re-execute phastCons to determine elements. I then filter regions e use to extract those regions with hal2maf again, to have a look at them.
They seem to be full of gaps. I don't know how familiar you are with such analysis, but I was wondering if I'm doing something wrong with my conversion. Do I have to sort the maf files or convert it into fastas, and how could I do that?

Thanks a lot
best
F