Usually we detect mutations by DNA-sequencing or whole exome sequencing, GATK http://www.broadinstitute.org/gatk/guide/best-practices is the commonly used pipeline for this purpose.
But RNA-seq data can also be used to call mutations in addition to detect the differentially expressed genes. However, the pipelines like GATK is not suitable for this kind of data.
A software
rnaseqmut
was developed by Wei Li in Harvard Dana-Farber cancer Insitute for this purpose
See the post here
http://allaboutbioinfo.blogspot.com/2013/09/detecting-mutations-from-rna-seq.html?showComment=1379423505178#c719553107057687822