#!/bin/bash #(java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/A_tigris8450.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/A_tigris8450.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/A_tigris8450.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/A_tigris8450.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/A_tigris8450.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/A_tigris8450.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/A_tigris8450.filtINDEL.vcf) & #proc1=$! #(java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/Atig003.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/Atig003.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig003.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/Atig003.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/Atig003.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/Atig003.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig003.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/Atig003.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/Atig003.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/Atig003.filtINDEL.vcf) & #proc2=$! #(java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/Atig001.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/Atig001.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig001.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/Atig001.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/Atig001.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/Atig001.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig001.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/Atig001.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/Atig001.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/Atig001.filtINDEL.vcf) & #proc3=$! #wait "$proc1" "$proc2" "$proc3" java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -T CombineVariants --variant $PATH/heterozygosity/gatk/training/filtSNP/A_tigris8450.filtSNP.vcf --variant $PATH/heterozygosity/gatk/training/filtSNP/Atig003.filtSNP.vcf --variant $PATH/heterozygosity/gatk/training/filtSNP/Atig001.filtSNP.vcf -o $PATH/heterozygosity/gatk/training/all_var/all_SNPs_0.vcf --excludeNonVariants --minimumN 1 java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -T CombineVariants --variant $PATH/heterozygosity/gatk/training/filtINDEL/A_tigris8450.filtINDEL.vcf --variant $PATH/heterozygosity/gatk/training/filtINDEL/Atig003.filtINDEL.vcf --variant $PATH/heterozygosity/gatk/training/filtINDEL/Atig001.filtINDEL.vcf -o $PATH/heterozygosity/gatk/training/all_var/all_INDELs_0.vcf --excludeNonVariants --minimumN 1 vcftools --vcf $PATH/heterozygosity/gatk/training/all_var/all_SNPs_0.vcf --remove-filtered LowQual --remove-filtered default_snp_filter --recode --recode-INFO-all --out $PATH/heterozygosity/gatk/training/all_var/all_SNPs_0 vcftools --vcf $PATH/heterozygosity/gatk/training/all_var/all_INDELs_0.vcf --remove-filtered LowQual --remove-filtered default_indel_filter --recode --recode-INFO-all --out $PATH/heterozygosity/gatk/training/all_var/all_INDELs_0 (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/A_tigris8450.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_0.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_0.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/A_tigris8450.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/A_tigris8450.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_0.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_0.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0_plots.pdf) & proc4=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/Atig003.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_0.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_0.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/Atig003.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/Atig003.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_0.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_0.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0_plots.pdf) & proc5=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/Atig001.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_0.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_0.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/Atig001.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/preprocessing/realigned_dedup_merged_bams/Atig001.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_0.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_0.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0_plots.pdf) & proc6=$! wait "$proc4" "$proc5" "$proc6" (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.bsqr_0.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.bsqr_0.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/A_tigris8450.bsqr_0.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/A_tigris8450.bsqr_0.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/A_tigris8450.bsqr_0.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.bsqr_0.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/A_tigris8450.bsqr_0.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/A_tigris8450.bsqr_0.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/A_tigris8450.bsqr_0.filtINDEL.vcf) & proc7=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/Atig003.bsqr_0.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig003.bsqr_0.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/Atig003.bsqr_0.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/Atig003.bsqr_0.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/Atig003.bsqr_0.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig003.bsqr_0.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/Atig003.bsqr_0.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/Atig003.bsqr_0.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/Atig003.bsqr_0.filtINDEL.vcf) & proc8=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/Atig001.bsqr_0.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig001.bsqr_0.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/Atig001.bsqr_0.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/Atig001.bsqr_0.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/Atig001.bsqr_0.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig001.bsqr_0.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/Atig001.bsqr_0.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/Atig001.bsqr_0.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/Atig001.bsqr_0.filtINDEL.vcf) & proc9=$! wait "$proc7" "$proc8" "$proc9" java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -T CombineVariants --variant $PATH/heterozygosity/gatk/training/filtSNP/A_tigris8450.bsqr_0.filtSNP.vcf --variant $PATH/heterozygosity/gatk/training/filtSNP/Atig003.bsqr_0.filtSNP.vcf --variant $PATH/heterozygosity/gatk/training/filtSNP/Atig001.bsqr_0.filtSNP.vcf -o $PATH/heterozygosity/gatk/training/all_var/all_SNPs_1.vcf --excludeNonVariants --minimumN 1 java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -T CombineVariants --variant $PATH/heterozygosity/gatk/training/filtINDEL/A_tigris8450.bsqr_0.filtINDEL.vcf --variant $PATH/heterozygosity/gatk/training/filtINDEL/Atig003.bsqr_0.filtINDEL.vcf --variant $PATH/heterozygosity/gatk/training/filtINDEL/Atig001.bsqr_0.filtINDEL.vcf -o $PATH/heterozygosity/gatk/training/all_var/all_INDELs_1.vcf --excludeNonVariants --minimumN 1 vcftools --vcf $PATH/heterozygosity/gatk/training/all_var/all_SNPs_1.vcf --remove-filtered LowQual --remove-filtered default_snp_filter --recode --recode-INFO-all --out $PATH/heterozygosity/gatk/training/all_var/all_SNPs_1 vcftools --vcf $PATH/heterozygosity/gatk/training/all_var/all_INDELs_1.vcf --remove-filtered LowQual --remove-filtered default_indel_filter --recode --recode-INFO-all --out $PATH/heterozygosity/gatk/training/all_var/all_INDELs_1 (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_1.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_1.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_0.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_1.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_1.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1_plots.pdf) & proc10=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_1.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_1.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_0.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_1.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_1.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1_plots.pdf) & proc11=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_1.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_1.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_0.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_1.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_1.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1_plots.pdf) & proc12=$! wait "$proc10" "$proc11" "$proc12" (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.bsqr_1.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.bsqr_1.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/A_tigris8450.bsqr_1.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/A_tigris8450.bsqr_1.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/A_tigris8450.bsqr_1.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.bsqr_1.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/A_tigris8450.bsqr_1.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/A_tigris8450.bsqr_1.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/A_tigris8450.bsqr_1.filtINDEL.vcf) & proc13=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/Atig003.bsqr_1.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig003.bsqr_1.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/Atig003.bsqr_1.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/Atig003.bsqr_1.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/Atig003.bsqr_1.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig003.bsqr_1.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/Atig003.bsqr_1.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/Atig003.bsqr_1.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/Atig003.bsqr_1.filtINDEL.vcf) & proc14=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/Atig001.bsqr_1.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig001.bsqr_1.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/Atig001.bsqr_1.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/Atig001.bsqr_1.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/Atig001.bsqr_1.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig001.bsqr_1.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/Atig001.bsqr_1.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/Atig001.bsqr_1.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/Atig001.bsqr_1.filtINDEL.vcf) & proc15=$! wait "$proc13" "$proc14" "$proc15" java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -T CombineVariants --variant $PATH/heterozygosity/gatk/training/filtSNP/A_tigris8450.bsqr_1.filtSNP.vcf --variant $PATH/heterozygosity/gatk/training/filtSNP/Atig003.bsqr_1.filtSNP.vcf --variant $PATH/heterozygosity/gatk/training/filtSNP/Atig001.bsqr_1.filtSNP.vcf -o $PATH/heterozygosity/gatk/training/all_var/all_SNPs_2.vcf --excludeNonVariants --minimumN 1 java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -T CombineVariants --variant $PATH/heterozygosity/gatk/training/filtINDEL/A_tigris8450.bsqr_1.filtINDEL.vcf --variant $PATH/heterozygosity/gatk/training/filtINDEL/Atig003.bsqr_1.filtINDEL.vcf --variant $PATH/heterozygosity/gatk/training/filtINDEL/Atig001.bsqr_1.filtINDEL.vcf -o $PATH/heterozygosity/gatk/training/all_var/all_INDELs_2.vcf --excludeNonVariants --minimumN 1 vcftools --vcf $PATH/heterozygosity/gatk/training/all_var/all_SNPs_2.vcf --remove-filtered LowQual --remove-filtered default_snp_filter --recode --recode-INFO-all --out $PATH/heterozygosity/gatk/training/all_var/all_SNPs_2 vcftools --vcf $PATH/heterozygosity/gatk/training/all_var/all_INDELs_2.vcf --remove-filtered LowQual --remove-filtered default_indel_filter --recode --recode-INFO-all --out $PATH/heterozygosity/gatk/training/all_var/all_INDELs_2 (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_2.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_2.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_1.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_2.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_2.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2_plots.pdf) & proc16=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_2.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_2.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_1.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_2.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_2.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2_plots.pdf) & proc17=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_2.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_2.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_1.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_2.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_2.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2_plots.pdf) & proc18=$! wait "$proc16" "$proc17" "$proc18" (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.bsqr_2.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.bsqr_2.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/A_tigris8450.bsqr_2.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/A_tigris8450.bsqr_2.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/A_tigris8450.bsqr_2.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/A_tigris8450.bsqr_2.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/A_tigris8450.bsqr_2.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/A_tigris8450.bsqr_2.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/A_tigris8450.bsqr_2.filtINDEL.vcf) & proc19=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/Atig003.bsqr_2.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig003.bsqr_2.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/Atig003.bsqr_2.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/Atig003.bsqr_2.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/Atig003.bsqr_2.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig003.bsqr_2.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/Atig003.bsqr_2.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/Atig003.bsqr_2.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/Atig003.bsqr_2.filtINDEL.vcf) & proc20=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2.realigned.dedup.merged.bam -stand_call_conf 30 -stand_emit_conf 30 -mbq 30 -o $PATH/heterozygosity/gatk/training/rawVAR/Atig001.bsqr_2.rawVAR.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig001.bsqr_2.rawVAR.vcf -selectType SNP -o $PATH/heterozygosity/gatk/training/rawSNP/Atig001.bsqr_2.rawSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawSNP/Atig001.bsqr_2.rawSNP.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "default_snp_filter" -o $PATH/heterozygosity/gatk/training/filtSNP/Atig001.bsqr_2.filtSNP.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T SelectVariants -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawVAR/Atig001.bsqr_2.rawVAR.vcf -selectType INDEL -o $PATH/heterozygosity/gatk/training/rawINDEL/Atig001.bsqr_2.rawINDEL.vcf; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T VariantFiltration -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -V $PATH/heterozygosity/gatk/training/rawINDEL/Atig001.bsqr_2.rawINDEL.vcf --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filterName "default_indel_filter" -o $PATH/heterozygosity/gatk/training/filtINDEL/Atig001.bsqr_2.filtINDEL.vcf) & proc21=$! wait "$proc19" "$proc20" "$proc21" java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -T CombineVariants --variant $PATH/heterozygosity/gatk/training/filtSNP/A_tigris8450.bsqr_2.filtSNP.vcf --variant $PATH/heterozygosity/gatk/training/filtSNP/Atig003.bsqr_2.filtSNP.vcf --variant $PATH/heterozygosity/gatk/training/filtSNP/Atig001.bsqr_2.filtSNP.vcf -o $PATH/heterozygosity/gatk/training/all_var/all_SNPs_3.vcf --excludeNonVariants --minimumN 1 java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -T CombineVariants --variant $PATH/heterozygosity/gatk/training/filtINDEL/A_tigris8450.bsqr_2.filtINDEL.vcf --variant $PATH/heterozygosity/gatk/training/filtINDEL/Atig003.bsqr_2.filtINDEL.vcf --variant $PATH/heterozygosity/gatk/training/filtINDEL/Atig001.bsqr_2.filtINDEL.vcf -o $PATH/heterozygosity/gatk/training/all_var/all_INDELs_3.vcf --excludeNonVariants --minimumN 1 vcftools --vcf $PATH/heterozygosity/gatk/training/all_var/all_SNPs_3.vcf --remove-filtered LowQual --remove-filtered default_snp_filter --recode --recode-INFO-all --out $PATH/heterozygosity/gatk/training/all_var/all_SNPs_3 vcftools --vcf $PATH/heterozygosity/gatk/training/all_var/all_INDELs_3.vcf --remove-filtered LowQual --remove-filtered default_indel_filter --recode --recode-INFO-all --out $PATH/heterozygosity/gatk/training/all_var/all_INDELs_3 (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_3.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_3.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_3.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_3.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_3.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_2.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_3.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_3.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_3.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_3_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_3.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_3_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/A_tigris8450.bsqr_3_plots.pdf) & proc22=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_3.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_3.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_3.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_3.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_3.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_2.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_3.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_3.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_3.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_3_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_3.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_3_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/Atig003.bsqr_3_plots.pdf) & proc23=$! (java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_3.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_3.recode.vcf -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_3.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T PrintReads -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2.realigned.dedup.merged.bam -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_3.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_3.realigned.dedup.merged.bam; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -I $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_2.realigned.dedup.merged.bam -knownSites $PATH/heterozygosity/gatk/training/all_var/all_SNPs_3.recode.vcf -knownSites $PATH/heterozygosity/gatk/training/all_var/all_INDELs_3.recode.vcf -BQSR $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_3.table -o $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_3_after.table; java -Xmx3g -jar /home/dut/bin/GATK/GenomeAnalysisTK.jar -T AnalyzeCovariates -R $PATH/fasta/bwa_reference/lizard_23Jun2015_piz6a_uppercase.fa -before $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_3.table -after $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_3_after.table -plots $PATH/heterozygosity/gatk/training/recal_BAMs/Atig001.bsqr_3_plots.pdf) & proc24=$! wait "$proc22" "$proc23" "$proc24" echo "Training Finished"