Hi there !
I am analyzing a set of WES tumor samples for which I don't have matched-normals, although I have 6 independent normal samples. As for the detection of CNVs, I first run CONTRA on the normal samples to create a baseline of normals (by executing baseline.py), and that was fine.
Furthermore, I run contra to detect somatic changes in CNV on the tumor samples, by using the baseline of normals (i.e., -c baseline_from_normal_samples.pooled2_TRIM0.2.txt). Apparently the execution of contra.py was OK, as I got no output errors.
Command line used (example for sample 1):
contra --minExon 100 --minReadDepth 5 --minNBases 20 --nomultimapped --plot --bed -c baseline_from_normal_samples.pooled2_TRIM0.2.txt --target ROCHE.bed --fasta $REFERENCE/hg19.fa --test $BAM/sample1.RECALIBRATED.bam -o sample1 --sampleName sample1
My question is regarding the plots I am getting in the Contra output. I would very much be interested in getting plots as the ones that are shown in figures 5A and 5B of the Contra paper (https://academic.oup.com/view-large/figure/83388120/bts146f5.jpeg), although I am not able to get them and those are the most common CNV output images. I am just able to get several plots with density information (https://www.dropbox.com/s/9avdq23q6wl5a63/PM_TP5_001.densityplot.20bins.pdf?dl=0).
Am I missing something in order to be able to get with Contra those figures that I am interested in?
Thank you very much in advance. Have a nice day !