3_select_variants

#!/bin/bash
#SBATCH --job-name=03_selectVariant         # Job name
#SBATCH --partition=highmem_p             # Partition (queue) name
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --mem=400gb                     # Job memory request
#SBATCH --time=150:00:00               # Time limit hrs:min:sec
#SBATCH --output=log_03_selectVariant.%j.out    # Standard output log
#SBATCH --error=log_03_selectVariant.%j.err     # Standard error log

#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=gb92068@uga.edu  # Where to send mail

cd $SLURM_SUBMIT_DIR

index_tray='/scratch/gb92068/muscadine_snp_calling/muscat_of_alexandra_snp_calling/trayIndex/'
sam='/scratch/gb92068/muscadine_snp_calling/muscat_of_alexandra_snp_calling/output/samDir/'


ml GATK/4.1.6.0-GCCcore-8.3.0-Java-1.8


##Select variants
gatk --java-options "-Xmx64g" SelectVariants -R $index_tray/VITMroTrayshed_v2_0_ChrRenamed.fasta -V $sam/raw_variants.vcf -select-type SNP -O $sam/raw_snps.vcf
gatk --java-options "-Xmx64g" SelectVariants -R $index_tray/VITMroTrayshed_v2_0_ChrRenamed.fasta -V $sam/raw_variants.vcf -select-type INDEL -O $sam/raw_indel.vcf