How parse collectReadCounts output in r?

Question

[Nemo]

I need to get read counts per gene. I am using GATK collectReadCounts method via following piece of code:

"gatk",
  "CollectReadCounts",
  "-I", paste0("./sorted-bams/D10.bam"),
  "-L", "chr1:11869-14409",
  "-imr", "OVERLAPPING_ONLY",
  "--format", "TSV",
  "-O", paste0("./collectReadCounts/DDX11L1.tsv")

It is running without any problem. I would like to parse the output in R (rstudio). How I can do it? I used read.table but gives me error and I think its not an appropriate method to do it. I would appreciate any idea.

[Istvan Albert]

add a few lines from the output to your post, plus be specific as to the error that you are getting