Convert BLAST output to gff format

Introduction

• This is a simple Shell script to convert BLAST output format 6 (tabular format with no headings) into gff format (contains mainly the start and stop positions) for downstream sequence extraction using bedtools.

Usage

% ./blastoutput2gff.sh FILENAME

• FILENAME must be in BLAST output format 6 with no headings (12 columns in total). Please refer to this in case you are unsure of the formats: https://www.ncbi.nlm.nih.gov/books/NBK279675/
• The gff outputs will be named as FILENAME.gff by default.