Scripts for parsing a VCF file resulting from bcf-tools merge
The Jupyter Notebook contains scripts to parse a VCF file resulting from bcftools merge.
This script generates a simplified VCF file as TSV.
The issue with the TSV file generated is that it keeps structural variants at the same position. We tried to correct this issue with a filter of 30 bp, it is optional right now.
The additional VCF file results from comparing tools
Input: a VCF file resulting from VCF-tools
Output: a TSV file containing info from the VCF