I have RNA-seq data from the BALB/c mouse strain.

Looking for the reference genome on Ensembl, I found that, the most recent version, GRCm38 was build using the C57BL/6J strain.

I suppose that, the PATCH files contains haplotypes and variation also from other strain, like balb/c.

Are these information on the primary assembly file?

If I want to, How can I use the patch files for building the index? Just concatenate the files?

Or use the toplevel file for indexing?

Thank you.
If your goal is to reduce the allele bias in RNA-seq read mapping then using PATCH files won't be of much help. You will have to generate a strain-specific reference genome in order to align your reads or use some sensitive aligner. BALB/c has been sequenced as a part of Mouse Genome Project and the variant calls (VCF) can be downloaded from the following page: http://www.sanger.ac.uk/resources/mouse/genomes/. There are around 4 million SNPs and around 0.8 million indels between C57BL/6J and BALB/c. Although most of these variants fall into the intergenic regions but it would be a god practice to try to align reads in a haplotype-sensitive manner. You will have to create a customize reference genome by substituting small SNPs and Indels, and then perform the alignment. Sanger provides a big vcf file for all the strains, so you will have to 1) first extract variants for BALB/c strain and 2) then substitute them into the reference genome. There are many relevant posts on Biostars that have discussed both of these steps in a detailed manner.