How to visualize reads at per base position for a SNP

Question

[Saad Khan]

Hi I want to visualize using R/bioconductor a position in the bam file which contains putative SNP. I want to see and visualize how the bases in the reads mapping at that position are distributed. How should I go about it. Or is there a solution already available.

[Ashutosh Pandey]

samtools tview is a quick way to visualize SNPs.

Answer 1

[Pierre Lindenbaum]

Call samtools tview from R (http://www.htslib.org/man/samtools/) with option -d T (output=TEXT).

Answer 2

[Zev.Kronenberg]

IGV does exactly what you want.

[Saad Khan]

I am looking for a more R based solution.

[Ying W]

I don't think these tools exist in R since everyone already uses IGV or UCSC for visualizing. The only NGS visualization package I can think of for bioconductor is gViz or ggbio but it probably doesn't do what you are looking for. You can look at coverage but I don't think you can look at individual SNPs or reads.