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Old 09-10-2010, 01:20 AM   #2
jeny
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Location: france

Join Date: Mar 2010
Posts: 16
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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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