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BAM format requirements

asked 2012-09-26 17:07:22 -0600

Patrick Gaffney gravatar image

What are formatting requirements for BAM files loaded into GenomeBrowse?

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answered 2014-08-12 15:00:42 -0600

Right, for our network BAM file reading, we assume the .bai file is located at file.bam.bai rather than file.bai.

I'm sorry that that assumption doesn't hold up in your situation.

For local BAM files, we can look at the file system and see if there is no file.bam.bai but there is a file.bai we can find the index file and move on.

We can not generate .bai files for remote sources as that requires reading the entire BAM file (which is as much work as downloading the file).

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answered 2014-08-11 05:43:08 -0600

Jorge Amigo gravatar image

updated 2014-08-11 05:47:00 -0600

if a file.bam has a file.bam.bai in the same folder it works perfectly, but if it has a file.bai instead it doesn't. it doesn't seem to generate the .bai on the fly, hence a "server replied: not found (error code 1)" message is provided. any way we can solve this issue?

PS: the file.bam we are trying to access is behind a htaccess restriction. the .bam is perfectly displayed as a valid data source once authenticated.

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answered 2012-10-01 20:37:24 -0600

We require the BAM file be sorted, that's it.

Often, pipelines that write bam files also write the bam index (BAI) file alongside it. Great!

If the BAI file is available, we will use it and you can immediately view the reads below the 10kb zoom window while we compute coverage data above that threshold.

If no BAI file is preset, we compute both the BAI and the coverage data in one pass.

Unfortunately, until that compute is finished, it's not possible to read any data in genomic coordinates and thus you won't be able to see any reads at any zoom level.

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Asked: 2012-09-26 17:07:22 -0600

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Last updated: Aug 12 '14