[BioC] Depth of Coverage and Base counts from BAM file

Chandu [guest] guest at bioconductor.org
Thu Aug 29 09:58:07 CEST 2013


Given BAM file, I like to get output something like below. Any ideas?

Chr     Position     DepthOfCoverage         BaseCounts
chr1   14112	   14	                         	A:0 C:0 G:0 T:14 N:0 
chr1   14113	   13		                	A:0 C:13 G:0 T:0 N:0 
chr1   14114	   11		                        A:0 C:0 G:0 T:11 N:0 
chr1   14115	   11		                 	A:10 C:0 G:0 T:1 N:0 

Many thanks in advance.

Best Regards

 -- output of sessionInfo(): 

R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base 

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