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Problems importing BAM files from IonTorrent Server

asked 2013-02-22 12:24:51 -0600

Francisco del Castillo gravatar image

When I try to load a BAM file from an IonTorrent run (unsorted, no BAI file), I get an Error Code 18 warning (Unable to match data in this source...). How can I work around this to index my BAM file

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answered 2013-02-22 13:22:54 -0600

Hi Francisco,

Unfortunately GenomeBrowse requires that your BAM file be at least sorted before it can be indexed and viewed within the software. We recommend using SAMtools or a similar BAM tool to have the file sorted.

Once the file is sorted you will want to make sure and have the corresponding reference sequence track for the species and build that corresponds to the your BAM file downloaded locally on your machine.

If you have human data from IonTorrent then you will need the "Reference Sequence, 1000Genomes" track for build GRCH_37_g1k downloaded prior to loading the sorted BAM file into GenomeBrowse. This particular genome build was just made available with the most recent version (v1.0.7) release of GenomeBrowse so you will need to make sure you are running this latest version.

If you are still having issues loading the file after having it sorted please let us know.

Thanks, Jami...

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Asked: 2013-02-22 12:24:51 -0600

Seen: 146 times

Last updated: Feb 22 '13