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  • how can I get the exome sequencing

    Sorry if this question may sound very simple, but I cant find the solution. I have a SAM file with an exome sequencing, all the short ILUMINA sequences aligned. I know how to get the variant file compared to a reference genome, but what I need is the whole exome sequence, not only the variants.

  • #2
    You can do --output_mode EMIT_ALL_SITES and then extract the sequence from there.

    However, the output is not phased. You can use ReadBackedPhasing in GATK to do the phasing but for now, it doesn't support indel. Anyone know of a better phasing tool??

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