Question

Converting Sam File To Hdf5

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12.1 years ago

Abhi ★ 1.6k

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

sam samtools bam • 3.7k views

ADD COMMENT • link updated 12.1 years ago by Pierre Lindenbaum 161k • written 12.1 years ago by Abhi ★ 1.6k

Ram · Answer 1 · 2012-03-10

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12.1 years ago

Pierre Lindenbaum 161k

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

ADD COMMENT • link 12.1 years ago by Pierre Lindenbaum 161k

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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

ADD REPLY • link updated 4.6 years ago by Ram 43k • written 12.1 years ago by lh3 33k

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

ADD REPLY • link 12.1 years ago by Abhi ★ 1.6k

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@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?

ADD REPLY • link 12.1 years ago by Steve Lianoglou 5.2k