Merge CNVnator and Lumpy to find out copy number variants

Question

[Mbillah]

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? Thank you

Answer 1

[Mant]

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.

For more info on lumpy read here: https://github.com/arq5x/lumpy-sv/blob/master/README.md

I'm trying to figure out how to choose the right -b flag in cnvanator_to_bedpes.py, which is "The total size of the resulting breakpoint centered on the call edge"...

[nitinra]

Do you know what format the genome file size should be for bedpe_sort.py? I tried using the reference file in fasta format and it returned a blank file.