I am running a ABBABABA test. Following the steps in the link http://www.popgen.dk/angsd/index.php/Abbababa
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 https://github.com/ANGSD/angsd/tree/master/R
How do I go about that… is it loaded with the module angsd/0.918?
Hope you can help!
Sorry I have I figured it out.
Hi Sushma, glad to hear you figured it out! Any chance you would post the solution in case someone else has the same issue?
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