1) I want to run star 2 pass pipeline: After running 1-star mapping, I got SJ.OUT.TAB for each library , now please suggest after concatenate all the SJ.out.tab files into one file, how to perform the filtering, and use only this filtered file.
2) ) Is it required to do Indel Realignment and base Recalibration while calling SNP from RNAseq data?
3) ) Which variant caller should I used, if I have multiple bam files. do I use Haplotype caller or GenotypeGVCFs by merging all bam file?
I will be thankful to you for helping me.