My aim is to find out copy number variants. I knew that CNVnator is enough to find out CNV. Recently I read a post from GitHub. Where they merge CNVnator and lumpy pipeline. Post link: Can anyone explain please?
This is the script to integrate CNVnator results information into Lumpy caller.
At the beginning it just uses CNVnator to obtain its results, then creates the files with these info in "Lumpy-friendly" files, removes "chr" in the calls (if there is such string), sorts them and at the end calls lumpy to work on its usual files (bam, discordants and splitters) and the newly created lumpy-readable CNVnator calls.