Fasta file for Whole exome sequencing analysis

Question

[tomer9w]

Hi all!

First time analyzing WES, wanted to make sure downloading the best suited reference fasta file. In the mouse gencode site (https://www.gencodegenes.org/mouse/release_M25.html) I saw there are multiple options:

1. Transcript sequences
2. Protein-coding transcript sequences
3. Protein-coding transcript translation sequences
4. Long non-coding RNA transcript sequences
5. Genome sequence (GRCm38.p6)
6. Genome sequence, primary assembly (GRCm38)

In this analysis, I would like to annotate the output variants, in order to count the number of NSM and synononymous mutations using SNPEFF package. The annoation part will use the SNPEFF available reference genome GRCm38.99.

Wanted to make sure I'm using the best reference fasta format. I started with 'Transcript sequences' (option number 1), is this the best option?

Thanks!

[GenoMax]

If you are doing whole exome sequencing then it would be best to get the co-ordinates (or a sequence file) from the vendor of the kit that was used.

[tomer9w]

Thanks GenoMax! So, using the reference from the kit vendor would be the best option. But, if it's not available, what would be the second best option?