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 !
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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