Tag next-generation sequencing

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.

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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.

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