Gini Coefficient and Lorenz curve to measure uniformity of coverage

Question

[am]

Hello, would you suggest me a nice tool to compute Gini index / plot Lorenz curve to estimate uniformity of coverage over the genome other than the R Package ‘ineq’ or the old R Package 'htSeqTools' ?

Thank you in advance!

Answer 1

[am]

Hi Federico, I kept using ineq or python code: https://github.com/auroramaurizio/my_DNA_seq_pipelines/blob/main/GINI_index/Snakefile. I also suggest you to check the bioconductor R package SCOPE https://www.bioconductor.org/packages/devel/bioc/vignettes/SCOPE/inst/doc/SCOPE_vignette.html#gini-coefficient.

HTH!

[abascalfederico]

Thank you! I finally used some code from my supervisor for the Lorenz curves, it's relatively easy, and DescTools::Gini to compute the gini coefficient. The input data was just 10Mbp of samtools depth

Answer 2

[abascalfederico]

Hi, did you find a program to do this?