I'm in the process of trying to figure out the 'best' method for looking at SNP/variant/indel calling in a set of paired-end Illumina rat RNAseq data that has been mapped using Bowtie to rn5 and converted to bam files. I have 2 groups, WT and mutant and have 6 biological replicates. I'm relatively new to RNaseq analysis so only have access to the main Galaxy server at usegalaxy.org and may be slightly naive in my understanding of the different tools available to me.
I believe the most common method for running SNP analysis is using the GATK tools but I believe there's only GATK beta tools currently available which uses the human b37 genome only. What are your thoughts on the best method for calling SNPs/Indels in this dataset using the current tools? Would Mpileup/Freebayes be the way to go?
In addition, what would be the best method for comparing the two groups, control vs mutant?
Any help on this would be greatly appreciated.