Converting Sam File To Hdf5

Question

[Abhi]

Hi Guys

Just curious to know if anyone has poked around with converting a sam file to hdf5 format. I am not sure how it compares to a bam file but I guess it would be interesting to compare if HDF5 format can make the computation on sam/bam files more efficient.

-Abhi

Answer 1

[Pierre Lindenbaum]

The BioHDF API seems to contain some references to the SAM/BAM format: http://www.hdfgroup.org/projects/biohdf/api_docs/html/structbioh5galignmentdata.html

[lh3]

FYI: http://sourceforge.net/search/index.php?group_id=246254&type_of_search=mlists&q=biohdf&ml_name%5B%5D=samtools-devel&form_submit=Search

[Abhi]

Pierre : thanks ..the link is a good place for me to start playing

[Steve Lianoglou]

@Pierre: The whole BioHDF movement hit my radar sometime in 2010, but I haven't heard much about it since then. Do you know if it's getting any traction anywhere? Do you know people trying to use it?