VQSR_1_SLURM.sh

#!/bin/bash
touch VQSR_1_STEP.sh
chmod 755 VQSR_1_STEP.sh
cat > VQSR_1_STEP.sh <<-EOF
#!/bin/bash -l
#SBATCH --job-name=VQSR_1_step
#SBATCH --mem-per-cpu=10000
#SBATCH --time=120:00:00
#SBATCH --account=mignot
#SBATCH --nodes=1
module load java/8u66
module load R/3.4.1
gatk="GenomeAnalysisTK.jar"
java -Djava.io.tmpdir=/local/scratch -jar \$gatk -T VariantRecalibrator -R ucsc.hg19.fasta \
-input $1.vcf \
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg19.sites.vcf \
-resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.hg19.sites.vcf \
-resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.hg19.sites.vcf \
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg19.vcf \
-an QD -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum -an InbreedingCoeff -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
-recalFile recalibrate_SNP_$1.recal -tranchesFile recalibrate_SNP_$1.tranches -rscriptFile recalibrate_SNP_plots_$1.R
EOF