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Hi Yadhu,

I am sorry you are having issues computing the coverage for your BAM file.

The gautil function for coverage computations does not directly support using the FASTA formatted reference sequence. The reference file must be converted to Golden Helix TSF format using the Convert Data Wizard as a first step before it can be used in conjunction with gautil functions.

If you launch GenomeBrowse and open the Add dialog you can click Convert... in the lower left corner of the Data Source Library to launch the converter. You would then add your FASTA file and follow the prompts to create the TSF reference sequence file. You can find specifics on the options for converting in our manual at the following link. http://doc.goldenhelix.com/GenomeBrowse/2.0.2/convertsourcewizard.html

Please let us know if you have any further issues.

Thanks, Jami...