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Old 08-10-2013, 01:52 AM   #1
Jolin
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Default Can I use a whole-genome SNV caller on exome sequencing data

Hi all,

I want to detect SNV in tumor and normal samples. And I tried to use "Somaticsniper", which is a whole-genome SNV caller. But my data is exome sequencing data. So I wondered whether a whole-genome SNV caller would fit exome sequencing data.

Look forward to your advice. Thank you~~~

T
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Old 08-10-2013, 06:12 AM   #2
Heisman
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I have not used Somaticsniper, but many callers will allow you to specify a list of regions for which to call SNVs. Read through the manual perhaps and see if that's allowed. Otherwise, it depends on the algorithm, but if Somaticsniper evaluates any given site in isolation without incorporating information from other areas throughout the genome (most SNV callers evaluate sites in isolation to my knowledge), then you can call SNVs in the entire genome and filter for the SNVs solely in exomic regions.

Last edited by Heisman; 08-10-2013 at 11:15 AM.
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Old 08-10-2013, 09:11 AM   #3
Bukowski
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Yes, I routinely use SomaticSniper on paired tumour/normal exome data.
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Old 08-11-2013, 06:56 PM   #4
Jolin
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Hi Heisman,

Thank you very much. Somaticsniper can not define the captured region. Your suggestion is quite good. I'm checking the algorithm now~~
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Old 08-11-2013, 06:57 PM   #5
Jolin
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Thanks a lot, Bukowski,
It's quite helpful
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Old 08-11-2013, 07:04 PM   #6
swbarnes2
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You might want to use something like BEDTools intersectBEd to filter your .bams, so that they only include your exomic target. That might make for cleaner data.
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