I am using GATK4 and run baserecalibrator but i do not get any output in pdf as mention in here https://gatkforums.broadinstitute.org/gatk/discussion/1297/no-plots-generated-by-the-baserecalibrator-walker?

a) GATK version 4.1.4

b) Exact GATK commands used

gatk_4.1.4.0 --java-options "-Xmx60g" BaseRecalibrator -R hg38.fasta -I paired_bwa_sortsam_addRG_markdup.bam --known-sites gatk_bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz --known-sites gatk_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --known-sites gatk_bundle/dbsnp_146.hg38.vcf.gz -O paired_bwa_sortsam_addRG_markdup_BQSR.table -BQSR paired_bwa_sortsam_addRG_markdup_BQSR.grp --plot_pdf_file paired_bwa_sortsam_addRG_markdup_BQSR.pdf

this -BQSR paired_bwa_sortsam_addRG_markdup_BQSR.grp --plot_pdf_file paired_bwa_sortsam_addRG_markdup_BQSR.pdf just add up after reading the topic as i mention

##apply BQSR
gatk_4.1.4.0 --java-options "-Xmx60g" ApplyBQSR -I paired_bwa_sortsam_addRG_markdup.bam --bqsr-recal-file paired_bwa_sortsam_addRG_markdup_BQSR.table -O paired_bwa_sortsam_addRG_markdup_BQSR.bam

The output is no error but no output in pdf to look for before and after baserecalibration step.

thank you