I'm currently performing differential expression analysis using alignment-free quantification using Kallisto. To do this, I need to create a Kallisto index using Ensembl's cDNA and ncRNA annotations available at the following two links:

ftp://ftp.ensembl.org/pub/current_fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz ftp://ftp.ensembl.org/pub/current_fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz

However, later on in my analysis I realized that I had multiple Ensembl gene IDs pointing to the same gene. For example, I was gettign results for both ENSMUSG00000026012 and ENSMUSG00000102412 which both map to Cd28. I realized that the reason for this error was due to the fact that the annotations I was using contained haplotypes.

I would like to remove these haplotypes, and to do this I believe that I need to rerun my analysis using a primary assembly. However, Ensemble doesn't have annotated cDNA and ncRNA FASTA files of the primary assembly. How can I filter these files to contain only genes present in the primary assembly? Is there a better way for me to solve this issue?