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You mean to ask if you can use the
samtools mpileuputility, surely? The command can be used anywhere you want :)What kind of RNAseq data do you have? What organism is it for, and are you aligning it to a reference or assembling it de novo?
Thanks for the reply Ram.
Yes, I am not sure if I can use mplieup for RNA-Seq.
I am working on mouse model, Illumina HiSeq 2500, STAR aligner and reference based alignment.
Please edit your question and add the above information to it. That way, people need not read through comments to get all relevant information.
I would advise you to follow the GATK best practices for variant calling in RNA-seq