Concat multiple CDS and binning, to show relative position of SNP in CDs. How to?

Question

[Chirag Nepal]

Hi all,

I have a list of CDS intersected with SNPs , like: intersectBed -wa -wb -s -a CDS.bed -b SNP.bed

chr15    78558585    78558635    NM_001130183    0    + chr15 8558615 8558616 rs1234
chr15    78562839    78563019    NM_001130183    1    + chr15 78563011 78563012 rs14444
chr15    78565437    78565541    NM_001130183    2    + chr15 78565521 78565522 rs13332

I could normalize the length of CDS and plot the distribution of each SNP, which is straight forward and easy to do. But this want give the position of SNP in the context of whole CDS.

I want to show the distribution of SNP with reference to whole concatenated CDS. The problem is that consecutive CDS also contains the information/position of introns and hence won't give me the perfect normalized position of SNPs. Any suggestions/ideas how to do this ?

Thanks in advance !

cheers