CONFIGEXAMPLE

repeat_species	arabidopsis
picard_dir	/path/to/picard-tools-1.114
gatk_dir	/path/to/GATK3-2-2
snpeff_dir	/path/to/snpEff
snpeff_cfg	/path/to/snpEff/snpEff.config
snpeff_species	athalianaTair10R23
genome	/path/to/snpEff/data/athalianaTair10R23/sequences.fa
genome_name	TAIR10
genome_date	20140808
known_gene	/path/to/snpEff/data/athalianaTair10R23/genes.gtf
known_snp	/path/to/arabidopsis_thaliana.vcf
gene_description	/path/to/TAIR10_functional_descriptions_20130831.txt
chrom_order	1,2,3,4,5,Mt,Pt

read1	/path/to/read-0_1.fastq
read2	/path/to/read-0_2.fastq
insert_size	300

read1	/path/to/read-1_1.fastq
read2	/path/to/read-1_2.fastq
insert_size	300

read1	/path/to/read-2_1.fastq
read2	/path/to/read-2_2.fastq
insert_size	300