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Setting up g2gtools on longleaf cluster

module load anaconda
git clone https://github.com/churchill-lab/g2gtools.git
cd g2gtools
git checkout develop
conda create -n g2gtools python=2
conda activate g2gtools
conda install numpy pysam cython natsort bx-python future
python setup.py install

Running g2gtools

Refer to http://churchill-lab.github.io/g2gtools/#overview for more detail.

First active the g2gtools environment

module load anaconda
conda activate g2gtools
  • Create VCI file from VCF (use --diploid for diploid analysis)
g2gtools vcf2vci -i <chr1.VCF> -f <chr1.fasta> -s <strain name> -o <output.vci>
  • Incorporate SNPs into the reference genome
g2gtools patch -i <chr1.fasta> -c <output.vci> -o <patch.fa>
  • Incorporate indels into the reference genome and get custom diploid genome for the sample
g2gtools transform -i <patch.fa> -c <output.vci> -o <transform.fa>
  • Liftover gene annotation onto sample coordinates
g2gtools convert -c <output.vci> -i <reference.coordinates.gtf> -o <sample.gtf>
  • Parse custom gene annotation into a G2G database file
g2gtools gtf2db -i <sample.gtf> -o <sample.db>

Note the process time is approximately 1 min/100,000 records. It is recommended to submit a bash file if the record number is large.

The record number can be checked by using

wc -l <sample.gtf>
  • Extract exons, transcripts, and gene regions from the custom sample genome
g2gtools extract -i <transform.fa> -db <sample.db> --exons > <sample.exons.fa>
g2gtools extract -i <transform.fa> -db <sample.db> --transcripts > <sample.transcripts.fa>
g2gtools extract -i <transform.fa> -db <sample.db> --genes > <sample.genes.fa>