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  • can we know target region of exome without bed file ?

    Now I have some exome data(bam files and vcf files) , but without the bed file.
    Can I get the target region just from the exome data?
    Or there are other alternatives I can try.

    Any advice would be very helpful.
    Thank you in advance.

  • #2
    Not really, no. You can take a guess that the regions with high coverage are likely target regions, but that would inevitably produce both false-positives and false-negatives.

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    • #3
      If you know what kit was used to enrich your exome then you'll be able to download a BED file from the web. I know that BED files are available for some of the most popular kits (Agilent SureSelect, Nimblegen, Ion TargetSeq etc) from the manufacturer's websites.

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      • #4
        You either need a .bed file of exons, or a .bed file of targets. The latter is better for QC, you really need to know what sequence the probes were aiming for before you can figure out how good a job they did at capturing that.

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