This is an old revision of the document!
https://github.com/diriano/ploidyNGS
Note that you will need a sorted bam file to run ploidyNGS
Script for running a ploidyNGS analysis on perun
#!/bin/bash
#$ -S /bin/bash
. /etc/profile
#$ -cwd
source activate ploidyNGS-preq
/scratch2/software/ploidyNGS/ploidyNGS.py -o outputfilename -b nameofsortedbamfile.bam
conda deactivate
Perun will immediately generate error messages that look dire if not fatal “fatal: not a git repository (or any parent up to mount point /misc) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).” but you can ignore these and the program continues to run
One of the options you will be interested in is -d 100 (default), –max_depth 100 (default)
Max number of reads kepth at each position in the reference genome (integer, default: 100) If you have low coverage you will need to change this otherwise you won't have many sites that qualify for examination.
Examine the tab output file. In particular, if the lines for Third and Fourth contain almost all 0.00 then they should be removed from the tab file, otherwise they mess up the histogram.
To see the sorted content of the Third and Fourth lines
grep Fourth myoutput.tab |cut -f4 |sort -n
grep Third myoutput.tab |cut -f4 |sort -n
To remove Third and Fourth lines from the tab
grep -v Fourth myoutput.tab |grep -v Third > mytabforhistogram.tab
Once satisfied with the tab you need to make a pdf (it is suppose to generate it automatically but it doesn't)
On the commandline
Rscript --vanilla /scratch2/software/ploidyNGS/ploidyNGS_generateHistogram.R mytabforhistogram.tab
This will generate a pdf called NA which you can transfer to your home computer to look at.