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Old 08-23-2010, 12:26 PM   #1
nirav99
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Location: Houston, TX

Join Date: Aug 2010
Posts: 10
Default Generating a BAM file from Illumina export files in CASAVa 1.7

Hi All,

I am trying to generate a BAM file from Illumina export files.

I used the CASAVA1.7 tool illumina_export2sam.pl. However, the resulting SAM file did not have sequence dictionary of the references. Moreover, the contig names end with ".fa", so if I use picard to generate sequence dictionary, I have to edit it and append ".fa" to contig name.

Thus, I am hoping that someone has a better solution for generation the BAMs from the export files. Please let me know.

Thanks !
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