Best way to realign / test other aligners with bams generated with casava

[KevinLam]

Hi
Long story short. Only got bams from casava (and misc other bams and files BUT no fastq) from seq provider ...
I actually wish to use Broad's best practices workflow on the data.

What are the best options for me?

cheers
kev

[dpryan]

You could just convert the BAM files to fastq (google "bam2fastq") and then realign as you would like.