Hey, I'm new to bioinformatics and I'm having some trouble creating an mpileup. Trying to create an mpileup for a bam file. When I create one using the tool on samtools, using default settings it looks incorrect when I try to view it on IGV. I have viewed the .bam file on IGV before creating the mpileup and it looks ok. I would appreciate any help! Thanks.
The first thing to double check is that the proper reference genome was selected for the option "Using reference genome: ?". This should be the same exact genome build used to create the mapped BAM dataset. https://wiki.galaxyproject.org/Support#Reference_genomes
If that does not resolve the problem, would you please explain more about what exactly is wrong and where you are working (Galaxy Main http://usegalaxy.org, a local, another public Galaxy instance). We may ask you to share a history from http://usegalaxy.org.
Thanks, Jen, Galaxy team