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

    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
    http://kevin-gattaca.blogspot.com/

  • #2
    You could just convert the BAM files to fastq (google "bam2fastq") and then realign as you would like.

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