Accessing SAM CIGAR strings in ShortRead (Bioconductor)

[mixter]

Hi,

I am looking for a function or accessor in the R/Bioconductor package ShortRead, or something that uses the same standard format, that is able to get me the CIGAR strings.

I'm commonly using readAligned(filename,path,type="BAM") to access BAM files in R, however I could not find on how to access the optional data using ShortRead.

I'm especially interested in "XM:Z:" (methylation call strings from recent Bismark SAM output) as a part of a standard AlignedRead object.


Many thanks in advance

[mtmorgan]

Use the Rsamtools library, readBamGappedAlignment or more directly scanBam. Use the 'what' argument of ScanBamParam() to specify what aspects of the bam file you want to read in. Ask on the Bioconductor mailing list for additional help.