tseemann / gbk2bcfgff

Convert Genbank to GFF compatible with "bcftools csq"

gbk2bcfgff

Convert Genbank to GFF compatible with "bcftools csq"

Introduction

A common task in bacterial genome analyis is comparing your genome to a reference genome. The differences are usually represented in a VCF file as variants such as SNPs at particular genome coordinates. However, the microbiologist is more interested in how these variants affect the proteins andf other features. This process is often refereed to as "consrquences".

The consequences, or effects, that each variant has on the genome has traditionally been performed using snpEff which requires Java and is challenging to use with your private reference genomes.

In recent years the standard htslib tool bcftools has quietly implemented support for calling consequences through its csq subcommand. However, it only accepts a vary particular GFF format which is not used in the microbial genomics world. The gbk2bcfgff tool presented here will convert our standard bacteiral Genbank format to a GFF that will work with bcftools csq.

Install

conda install -c bioconda bcf2bcfgff  # COMING SOON

Quick Start

FIXME.

References

• bcftools csq manual
• csq.c comments

Author

Torsten Seemann