I am new to variant analysis. I have mutation induced RNAseq samples data which has been aligned to reference transcriptome and obtained a bam file which has been sorted. For every transcript I would like to count the number of mutated reads aligned to reference transcript. For an example, number of reads on which base C has been mutated to A at every position along the transcript.
Is it possible to achieve this using samtools and vcf tools.
Kindly guide me