Software for SNP zygosity and loss of heterozygosity

Question

[ceruleanivy]

I want to create a scatterplot with all the observed variant frequencies, but I cannot get the chromosome band on the X-axis with conventional software (SPSS, Excel). I'm interested in putting all chromosome bands (the whole human genome) in the X-axis as I'm doing targeted sequencing, but most examples that I've found contain only one chromosome like here

http://doc.goldenhelix.com/SVS/tutorials/roh_analysis/_images/heat-map-plus-b-allele-large.jpg

Answer 1

[Jan Oosting]

You can have a look at the bioconductor quantsmooth package.

It has plots to show chromosome bands together with your own data.

[ceruleanivy]

I have the raw output from IonTorrent but I cannot find instructions on how to prepare the input file for prepareGenomePlot (if that function is right for my case).