Hej all,
I have a vcf file that contains several SNPs and now I want to see, whether these SNPs are evenly distributed over the reads of the bam file from which I got the SNPs. Specifically, I want to plot the number of SNPs over read position, which means that on the x-axis I have all the bases of a read (in the case of Illumina HiSeq 100 bases) and on the y-axis the cumulative number of SNPs that were found on that position. An example is shown in this paper, figure 2: biomedcentral.com/1471-2164/12/150.
I am wondering whether there is some tool around for doing this or whether I have to write a script on my own. If so, is there a package in R with which I can do that (I am used to R but don't have much experience with perl)?
I have a vcf file that contains several SNPs and now I want to see, whether these SNPs are evenly distributed over the reads of the bam file from which I got the SNPs. Specifically, I want to plot the number of SNPs over read position, which means that on the x-axis I have all the bases of a read (in the case of Illumina HiSeq 100 bases) and on the y-axis the cumulative number of SNPs that were found on that position. An example is shown in this paper, figure 2: biomedcentral.com/1471-2164/12/150.
I am wondering whether there is some tool around for doing this or whether I have to write a script on my own. If so, is there a package in R with which I can do that (I am used to R but don't have much experience with perl)?