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-   -   Generating a BAM file from Illumina export files in CASAVa 1.7 (http://seqanswers.com/forums/showthread.php?t=6525)

nirav99 08-23-2010 12:26 PM

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 !

jeny 09-10-2010 01:20 AM

Hi,

I have not tried it for the moment, but you could use CASAVA-1.7 and samtools to do this.
1 - run GEARLD analysis with the option ''WITH_SORTED'' into config.txt file
2 - install samtools
3 - use run.pl CASAVA script with option --cmdSamtools path_to/samtools (executable) and with ''--targets all bam''

You can find informations into User Guide, Chap.5
Hope that help.
Regards


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