FORUMTry to do Abbababa analysis using angsd/0.918 and Rscript
sjossey asked 12 months 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 12 months ago

Sorry I have I figured it out.

jrosner Staff replied 12 months 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 12 months 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 12 months ago