Question: Variant analysis help
gravatar for cjain
21 months ago by
cjain10 wrote:


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

snp variants rna • 552 views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson25k • written 21 months ago by cjain10
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Try running mpileup within Galaxy. This will produce the proper 6 or 10 column input. Assign the datatype "pileup" as needed before using downstream tools.

For Native Variant Caller and FreeBayes, both have the option of using a custom reference genome from the history. This is the first option on both tool forms. How to:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k
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