GATK 220.127.116.11 AnalyzeCovariates
The csv produced by AnalyzeCovariates is invalid. It doesn't escape commas in fields, resulting in an error in the R script.
If you have a comma in the readgroup in a BAM, this will happen.
It should produce valid csv files, and then be able to properly produce the plots.
Commas in read group names result in malformed (unescaped) csv where it's impossible to parse fields properly. This results in the following R script error:
Error in read.table(file = file, header = header, sep = sep, quote = quote, : more columns than column names