FORUMTry to do Abbababa analysis using angsd/0.918 and Rscript
sjossey asked 2 years ago

I am running a ABBABABA test. Following the steps in the link
I ran the command
$ module load nixpkgs/16.09 intel/2018.3 angsd/0.918
$ angsd -out out -doAbbababa 1 -bam bamfilelist -doCounts 1 -useLast 4
That gives an output file out.abbababa
now I need to run a Rscript, jackKnife.R, from
How do I go about that… is it loaded with the module angsd/0.918?
Hope you can help!

1 Answers
Best Answer
sjossey answered 2 years ago

Sorry I have I figured it out.

jrosner Staff replied 2 years ago

Hi Sushma, glad to hear you figured it out! Any chance you would post the solution in case someone else has the same issue?

sjossey replied 2 years ago


I copied pasted the Rscript from the site…somehow the wget did not work and ran it with a bamlist with only 3 bamfile and excluding the outgroup

My command :
$ Rscript ./jackKnife.R file=out.abbababa indNames=bamfilelist3 outfile=outJack


jrosner Staff replied 2 years ago