VQSR no r file being created

Question

[geneart$$]

Hi ,

I have r module loaded in the path I am running my scripts , yet the --rscript all_jointcalls.AS.plots.R

is not even created !

Is there something I am missing? Here is my command and I am running GATK/4.1.8.0

gatk VariantRecalibrator \
  -V ../all_jointcalls_sorted.vcf \
  -AS \
  --trust-all-polymorphic \
  -tranche 100.0 -tranche 99.95 \
  -tranche 99.9 -tranche 99.8 \
  -tranche 99.6 -tranche 99.5 \
  -tranche 99.4 -tranche 99.3 \
  -tranche 99.0 -tranche 98.0 \
  -tranche 97.0 -tranche 90.0 \
  -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR \
  -mode SNP \
  -max-gaussians 6 \
  -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_subset3.3.hg38.vcf.gz \
  -resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_subset_omni2.5.hg38.vcf.gz \
  -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_subset_phase1.snps.high_confidence.hg38.vcf.gz \
  -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 Homo_sapiens_subset_assembly38.dbsnp138.vcf.gz \
  -O all_jointcalls_sorted_AS.recal \
  -tranches-file all_jointcalls_sorted_AS.tranches
  -rscript-file  all_jointcalls.AS.plots.R

[Jeremy Leipzig]

use two-dashes -- for long arguments, one - for short arguments https://gatk.broadinstitute.org/hc/en-us/articles/360036510892-VariantRecalibrator

[geneart$$]

Thankyou for the reply Jeremy, but thats not it. I tried with the -- and yet no rscript file is generated !

[Jeremy Leipzig]

is anything being generated or displayed? is it running for any length of time?

[geneart$$]

Thankyou Jeremy and rbagnall for your replies ! Yes the VQSR actually ran for a bit but gave me a truncated file so the end of the file actually had not shown the memory used although it did say : Tool returned: true" It was indeed the backslash that I had missed !! Small annoying things...but thankyou again for your time! Best

Answer 1

[rbagnall]

Is the all_jointcalls_sorted_AS.tranches file made?

have you put the \ afterwards, to separate from the --rscript-file command?

If the all_jointcalls.AS.plots.R file is created, try to run it afterwards, with

Rscript /path/to/all_jointcalls.AS.plots.R