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 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!
Thanks,
Sushma

1 Answers
Best Answer
sjossey answered 12 months ago



Sorry I have I figured it out.
Thanks,
Sushma

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

Sure!

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

Thanks,
Sushma

jrosner Staff replied 12 months ago

thanks!