Can not generate tranches plot after VQSR

Question

[Gerlumen]

Hello!

I have encountered with a strange issue when trying to analyze VariantRecalibrator output. I can not generate or find an R-script file of *.tranche output. At the same time i have no problems with scatter-plots generation an further import in Rstudio.

I am using the following commands:

 gatk VariantRecalibrator \
   --reference ref_genome/hg38_v0_Homo_sapiens_assembly38.fasta \
   --variant VARIANTS.vcf.gz \
   --resource:hapmap,known=false,training=true,truth=true,prior=15.0 sites4vqsr/resources_broad_hg38_v0_hapmap_3.3.hg38.vcf.gz \
   --resource:omni,known=false,training=true,truth=false,prior=12.0 sites4vqsr/resources_broad_hg38_v0_1000G_omni2.5.hg38.vcf.gz \
   --resource:1000G,known=true,training=true,truth=false,prior=10.0 sites4vqsr/resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gz \
   --use-annotation QD --use-annotation MQ --use-annotation MQRankSum --use-annotation ReadPosRankSum --use-annotation FS --use-annotation SOR \
   --mode SNP \
   --output VARIANTS_SNPs.recal \
   --tranches-file VARIANTS_SNPs.tranches \
   --rscript-file VARIANTS_SNPs.plots.R

Could you help with an advice, please?

[Pierre Lindenbaum]

t. I can not generate or find an R-script file of *.tranche output.

what is the exact error message with the stack exception , if any, please.

[Gerlumen]

Hello, Pierre! Thank you, for acknowledging my post :) There is no error messages during processing. I am just having VARIANTS_SNPs.tranches generated and no file with .R extension which would contain script for tranches visualisation in Rstudio. It seems like --rscript-file produces script for scatter-plots only. I have to say, that I am testing variant calling pipeline here and used only two wgs samples for that (in order to speed up testing steps). Is it possible that “tranches.R” generation depends on sample batch size? Thanks!

[Ren]

I also have this problem! There is only a file.R output for SNP scatterplot visualization. Is there a missing argument? I get a brief error saying that I don't have ggplot loaded on my hpc module, but I'm not sure why that would prevent the tranche r script from being created.

[Ram]

Don't add answers when you're not answering the question. Use Add Comment/Add Reply instead as appropriate. I've moved your post to a comment this time, please be more mindful in the future.