SNF2JSON

This tool is a simple file converter that takes a Sniffles (SNF) file and converts it into a JSON like object (SNFJ). The purpose of this converter is to make it easier to work with the Sniffles file format in other tools such as Spectre, which is a long read copy number variation (CNV) caller.

Functionality: To preserve the original data structure of the SNF file, the pickled objects withing the file are converted into a JSON like object structure, which can easily be loaded into a Python dictionary.

Installation:

pip install snf2json

Usage:

For compression use the .gz extension in the output filename.

snf2json <sample.snf> <new_sample.snfj.gz>

or

snf2json <sample.snf> <new_sample.snfj>