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Plot are not generated by VariantRecalibrator

Sarah61Sarah61 PakistanMember

I am using variantrecalibrator to get VQSLOD. This is my command.

gatk VariantRecalibrator -R new_hg38.fa \
-V allsample.vcf \
--resource hapmap,known=false,training=true,truth=true,prior=15.0:hapmap_3.3.hg38.vcf.gz \
--resource omni,known=false,training=true,truth=false,prior=12.0:omni2.5.hg38.vcf.gz \
--resource 1000G,known=false,training=true,truth=false,prior=10.0:thouzndG_phase1.snps.high_confidence.hg38.vcf.gz \
--resource dbsnp,known=true,training=false,truth=false,prior=2.0:All_20180418.chr.hg38.vcf.gz \
-an QD \
-an MQ \
-an MQRankSum \
-an ReadPosRankSum \
-an FS \
-an SOR \
-mode SNP \
-O output.snp.recal \
--tranches-file output.snp.tranches \
--rscript-file output.snp..plots.R

Script file is produced by tool. Also I installed ggplot2 in home directory. But pdf plots are not produced. Can someone tell me what to do about this issue?

Best Answer


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