Variants obtained from RNAseq ?

[memento]

According to the title:
Is there any existing pipeline that could extract variants (SNPs/somatic mutations) from RNAseq bam file ? Thanks in advance.

[Dario1984]

If it's from RNA, how do you know it's not caused by RNA editing ? To determine changes in the genome you need to sequence the DNA.

[Bukowski]

According to the title:
Is there any existing pipeline that could extract variants (SNPs/somatic mutations) from RNAseq bam file ? Thanks in advance.

It's clearly perfectly possible: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760790/ it's just a shame this paper wasn't stacked against an exome sequencing dataset or SNP chip for validation.

There is another paper I'm aware of : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898068/ which stacks the results against good depth whole genome sequencing. It's an interesting read.

[memento]

It definitely is a good read! Thanks!

[Milan Radovich]

Take a look at the SNVMix2 software. It was designed for calling variants from RNA-seq and was used in two NEJM articles.