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Viewing .BAM files

Dec 26, 2014 at 5:32 PM
Is there a way to view .BAM files with the Excel BIO tool?
Dec 27, 2014 at 11:18 PM
Hi Residentx10
The excel tool is not set up at present for BAM files. it is mainly set up for viewing and manipulation of nucleotide and amino acid sequences drawn from fasta and genbank files. What sort of work do you do? The library does have support for BAM parsing as I think mark has pointed out, but there is no default viewer for these files.

cheers
jh
Dec 28, 2014 at 2:41 AM
Edited Dec 28, 2014 at 2:42 AM
Hi,

Thanks for the reply. In the past, fasta and genbank was fine but we're starting to use lots of Illumina Genetic equipment now in WASHDC and they use .bam. There's a bam tookkit, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106182/
https://github.com/pezmaster31/bamtools but I love viewing this stuff in Excel.

Also, do you know if OuterCurve is actually updating these tools? I might join next year now that I can contribute.
Jan 19, 2015 at 1:23 PM
Hi Residentx10 - apologies for the delay in replying to the message; some holidays and travel. Back on deck now. We'd welcome involvement if you want to contribute. We can get you started pretty easily. Just post when you are ready. .NET Bio does have some facilities for parsing BAM files which you could certainly build on. The class is in the Bio.IO.BAM namespace. The description is as follows: BAMParser reads from a source of binary data that is formatted according to the BAM file specification, and converts the data to in-memory SequenceAlignmentMap object. Documentation for the latest BAM file format can be found at http://samtools.sourceforge.net/SAM1.pdf

cheers
jh