[Bioc-sig-seq] Rsamtools scanBam output to Bam

[Martin Morgan]

On 04/12/2010 09:35 AM, burak kutlu wrote:
> Hi Is there a way to create a SAM file from the output of scanBam
> from Rsamtools? The reason we would like to do is use IGV to
> visualize a subset of regions in a large Bam file using load2newIGV
> function from SRAdb. For this, we will need to put the list structure
> back to SAM format. Please let me know if this is enough to give you

no not at the moment; this is on the to do list. There is filterBam
which does a round-trip (no R interaction) though here it might make as
much sense to use samtools from the command line.

Martin

> an idea what we are trying to achieve. Thanks in advance -burak
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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