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Generating a BAM file from Illumina export files in CASAVa 1.7

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  • 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 !

  • #2
    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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