Creating GATK VQSR plots

Posted on 2013-05-15 15:38:53
by Geert Vandeweyer

Loading Content

Creating GATK VQSR plots

Posted on 2013-05-15 15:38:53
by Geert Vandeweyer

GATK provides nice plots on the gaussian distributions used by the variant quality recalibration tool. 

However, coverting the R-scripts to the actual pdf plots proved not so easy, and I couldn't find any documentation on the required versions of gatk/R/ggplot2 for this to work. 

After some trail-and-error, I found the following combination of tool versions to work for me on ubuntu 10.04 LTS (all R-packages compiled from source and fetched from the CRAN archives) 

• GATK : 2.4.9-g532efad
• R : 2.14.0
• plyr : 1.7.1
• reshape : 0.8.0
• ggplot2 : 0.8.9

Typical errors in other combinations included: 

• Error in scale_labels.continuous(scale, breaks) :Breaks and labels are different lengths
• could not find function "theme_rect"
• The following `from` values were not present in `x`: col, color, pch, cex, lty, lwd, srt, adj, bg, fg, min, max

bioinformatics, GATK, Installation, NGS, NGS, R, Rcran, Ubuntu