What VCF file to use when using crossed mouse strains?

Question

[jrose]

Hi,

I am new to working with mouse data. I am analyzing mouse RNA-Seq data from mice which are crosses between FVB and CAST strain (one parent is FVB and one is CAST). When doing base quality re-calibration (I am using BaseRecalibrator), for example, I am wondering, what VCF do I use? I have the FVB and CAST vcf files from the Sanger institute, found here, but do I just merge them? How? I am used to using human data where I would just use dbSNP. But now that I am using a cross between two strains, how do I merge the two VCFs to be used?

Answer 1

[Asaf]

I'm sorry I can't directly answer your question but I have some pointers. You might want to look at Churchill Lab GBRS pipeline (paper, github) it's a bit outdated (uses Bowtie1 for instance). A couple of years back I wrote a Nextflow pipeline to run GBRS but it requires data files that I couldn't find online right now (Churchill ftp site doesn't respond right now). I think that the way to do it is by using Salmon with both transcripts but I haven't tested it.

Answer 2

[jrose]

Thanks! I was pretty set on using the Phaser tool for various reasons but I will checkout GBRS as it seems like a great guide.