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gautils coverage for Bam files

asked 2015-03-05 10:49:28 -0600

Benjamin Brett
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I am trying to run gautils to precompute all of the files for GenomeBrowse. Currently I have it working on the vcf files, but when I try and process the bam I always get the error listed below. If I add the bam files to GenomeBrowse it has no issues generated the needed files and gives an error one link can not be added but still loads the file just fine. Any thoughts?

Unable to find reference sequence source for build: GRCh_37,Chromosome,Homo sapiens Ran into errors: Unable to match data in this source with an existing reference sequence. Reference sequence must have matching chromosome names and lengths.

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answered 2015-03-06 10:26:05 -0600

Benjamin Brett
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Solved with help from the support team.

Ensure that you have the tsf files properly installed in the correct directory. If the files are present but still getting the error, the files might be corrupted (my problem). Download the files again. If the files are downloaded on windows and transferred to Linux no conversion of line endings is needed.

Thanks!

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Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.

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Asked: 2015-03-05 10:49:28 -0600

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Last updated: Mar 06 '15

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