There are a lot of resources on the internet that describe how to convert bam files to fastq files for realignment, but many of them are using different methods and different tools. I have tested and evaluated many of these conversion tools and here are my findings.
Are you a programmer trying to figure out how to use a Windows computer for your work? Here are the programs I’ve been using for the past few years that have served me pretty well over the years.
Variant Effect Predictor’s command line program may seem intimidating to beginners, but is actually not that bad. Keep reading to see what I have learned from my experience working with command line VEP.