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Old 10-01-2013, 01:51 AM   #1
cjo4m4fm
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Location: taiwan

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Default 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.
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Old 10-01-2013, 03:03 AM   #2
dpryan
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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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Old 10-01-2013, 06:00 AM   #3
sophiespo
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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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Old 10-01-2013, 11:19 AM   #4
swbarnes2
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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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