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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.

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