GATK CNV Pipeline not plotting all discovered segments - PlotModeledSegments

Question

[taylor.falk3]

Hi all, I'm using GATK version 4.1.4.0 and this GATK tutorial to discover and plot some CNVs in a matched tumor/normal. Most of the CNVs have been correctly discovered and plotted, but there's a problem in chromosome level. The modelFinal.seg and cr.seg files correctly list the high CNV in chromosome 11:

CONTIG  START   END NUM_POINTS_COPY_RATIO   *MEAN_LOG2_COPY_RATIO*  
11  68205061    68568153    61  *3.301253*  
11  68571116    68677439    20  *3.906589*  
11  68716381    69533794    42  *4.311234*  
11  69824572    70249114    79  *3.446989*

But, these do not show up on the plot for modeled segments, on a copy ratio scale of 0 to 4:

I've reduced the minimum contig length from the default of 1,000,000 to 100,000, since these are relatively shorter contigs, but still no luck. Any thoughts?

Here's my current command for this step:

gatk PlotModeledSegments
--denoised-copy-ratios /practice/output/TP-01.denoisedCR.tsv
--allelic-counts /practice/output/TP-01.hets.tsv
--segments /practice/output/TP-01.modelFinal.seg
--sequence-dictionary /Resources/human_g1k_v37_decoy_plus_virus.dict
--minimum-contig-length 100000
--output /practice/output_plots/
--output-prefix 1_length_contig

Answer 1

[taylor.falk3]

It turns out that the plotting stops at 4, so I edited the R script to accommodate for the largest log2 copy ratio! Now I can far higher.