Q:
I am trying to find Allel specific expression from a hybrid mouse RNA-Seq. I
have the complete genome of the two parental strains and the corresponding
SNPs and Indels as vcf format. I don’t have a complete genome and genotype
for the hybrid mouse.

I am looking to your AllelSeq tools you have published and attempted to
create a custom genome using vcf2diploid_v0.2.6a. Would you please guild me
OR forward to someone in your group who will guide me if the tools will be
useful in such context? I see the tool was developed with Trios.

A:
AlleleSeq/vcf2diploid can be used both with trios and with single samples.
Either way, you would need to have a .vcf for the sample (hybrid mouse) in order to use the tools though.