Detecting Genomic Variations (SNPs and indels) from the RNA-Seq FASTQ files.
The pipeline is created as referring to GATK's RNAseq short variant discovery (SNPs + Indels). Please be noticed that we deploy HISAT2 for alignment instead of STAR to save memory consumption. Please be noticed that it won't work with any other organisms but human.
Please setup the pipeline to run GATK on the RNA-Seq data.