Which fasta file for Variant Calling using RNASeq

Question

[andrebolerbarros]

Hey everyone,

I want to perform variant calling using transcriptomic samples. I will use the recommended pipeline from GATK (https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels).

For the 2-pass alignment step with STAR, I was considering to use the same genome that I used for the gene counts step (dna.primary.assembly), but I got the idea this may not be ideal - Fasta file and GTF file for STAR alignment.

I wanted to confirm if I'm using the right file or not.

Thanks in advance.