I am trying to identify variants using data from a BAM file generated from an RNA-Seq experiment (not DNA-seq). I first tried to do so by making a pileup file using the BAM file as an input and a reference genome that I provided. When I tried to filter the pileup file, that command did not go through. I wonder if the error is due to the fact that pileup file I got had 5 columns, not six or ten. If so, is there a workaround?
I also alternatives to get the desired results using Native Variant Caller and FreeBayes. These tools offer a number of reference genomes from a drop-down menu, but don't appear to give me the option to input my own reference genome. Again, is there a solution to this?
Chaitanya Jain Associate Professor University of Miami