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VCF file size is not reduced after running 'ApplyRecalibration'
I was expecting the "ApplyRecalibration' to reduce the VCF files output by Haplotypecaller. Below is my command line for VariantRecalibrator and ApplyRecalibration. I was wondering if I did anything wrong or the VCF file size does not always get smaller? or any suggestions to improve my commandlines?
java -Xmx4g -Djava.io.tmpdir=/Volumes/tempdata1/tonywang/GATK_temp -jar $CLASSPATH/GenomeAnalysisTK.jar \ -T VariantRecalibrator \ -R GATK_ref/hg19.fasta \ --input ../GATK/raw_variants_snps_indels-3.vcf \ -nt 6 \ -resource:hapmap,known=false,training=true,truth=true,prior=15.0 GATK_ref/hapmap_3.3.hg19.vcf \ -resource:omni,known=false,training=true,truth=true,prior=12.0 GATK_ref/1000G_omni2.5.hg19.vcf \ -resource:1000G,known=false,training=true,truth=false,prior=10.0 GATK_ref/1000G_phase1.snps.high_confidence.hg19.vcf \ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 GATK_ref/dbsnp_137.hg19.vcf \ -an QD -an MQRankSum -an ReadPosRankSum -an FS -an DP \ --maxGaussians 4 \ --numBadVariants 2000 \ -mode SNP \ -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \ -log ../GATK/VQSR/log/raw_variants_snps-3_snps_recal.log \ -recalFile ../GATK/VQSR/SNPs/snps-3_snp.recal.vcf \ -tranchesFile ../GATK/VQSR/SNPs/snps-3_snp.tranches \ -rscriptFile ../GATK/VQSR/SNPs/snps-3_snp_recal.plots.R java -Xmx6g -Djava.awt.headless=true -jar $CLASSPATH/GenomeAnalysisTK.jar \ -T ApplyRecalibration \ -R GATK_ref/hg19.fasta \ -nt 5 \ --input ../GATK/raw_variants_snps_indels.vcf \ -mode SNP \ --ts_filter_level 99.0 \ -recalFile ../GATK/VQSR/SNPs/snps-3_snp.recal.vcf \ -tranchesFile ../GATK/VQSR/SNPs/snps-3_snp.tranches \ -log ../GATK/VQSR/SNPs/filtered/snps-3_snp.recal_filtered.log -o ../GATK/VQSR/SNPs/filtered/snps-3_snp.recal_filtered.vcf