Tri-hybrid cross reveals new major hybrid incompatbility locus between D. melanogaster and D. simulans.

These are the scripts and make files that I used for processing genomic data for our publication on mapping hybrid incompatibility genes. When we have a link to the paper, I will include that here.

Requirements

• trimmomatic
• java version 1.8
• GATK 3.6
• samtools
• picard tools
• bwa

Pipline

• trim reads
• align to the reference genome
• sort the reads
• index
• merge bam files
• call variants with GATK
• build VCF file from SNP table

Use

The "make_wrapper.sh" in /scripts/local/ should contain all the parameters that are required for going from fastq files to a vcf, given the reference genomes. The scripts in /analysis/ are for use once there is a vcf. There is an R script for making the plots from correctly parsed SNP tables.

There are also a series of helpful commands for running these programs on a SLURM managed cluster. This was run on the CHPC at the University of Utah, so your expereinece may differ. They are located in /scripts/kingspeak/