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.
2 answers
Call samtools tview from R (http://www.htslib.org/man/samtools/) with option -d T (output=TEXT).
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Pierre Lindenbaum
IGV does exactly what you want.
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Zev.Kronenberg
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.
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samtools tview is a quick way to visualize SNPs.