I am using a whole exome sequencing dataset to look for potential pathogenic mutations. Overall, I have good coverage, but some regions of interest do not have good coverage and generate a false negative result. Is there a way to check coverage in a list of genes using galaxy to know if any have poor coverage? Right now I am checking by looking at the genes of interest in the UCSC genome browser, but that is very time consuming. Any suggestions are appreciated.
The tool groups DeepTools and BEDTools at http://usegalaxy.org have several tool options for calculating coverage in BAM datasets. See the tool forms for links to usage help and more.
Others are welcome to comment about their favorite tools in these groups or alternates!
Thanks, Jen, Galaxy team