phase_snps_G1.srun

#!/bin/bash
#SBATCH --partition=short        ### Partition (like a queue in PBS)
#SBATCH --job-name=phase_genome_G1      ### Job Name
#SBATCH --output=phase_genome_G1.out         ### File in which to store job output
#SBATCH --error=phase_genome_G1.err          ### File in which to store job error messages
#SBATCH --time=0-24:00:00       ### Wall clock time limit in Days-HH:MM:SS
#SBATCH --nodes=1               ### Node count required for the job
#SBATCH -n15

# This command was ran to phase SNPs for input to MVFtools

module load easybuild
module load Java/1.8.0_131

java -Xss5m -Xmx8g -jar /projects/streisfeld/mchase2/genome_reseq/scripts/beagle.08Jun17.d8b.jar gt=/projects/streisfeld/mchase2/genome_reseq/genomeV1/var_calls/genome_V1/pairwise_comps/all_9_taxa_G1_vars.vcf map=/projects/streisfeld/mchase2/genome_reseq/genomeV2/phasing/post_chrom_map.map.txt nthreads=15 window=100000 overlap=10000 impute=false out=/projects/streisfeld/mchase2/genome_reseq/genomeV1/var_calls/genome_V1/phasing/phased_snps_WG_G1.vcf