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Old 06-12-2010, 07:37 AM   #1
foxyg
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Default The workflow after alignment

Hi everyone, I am relatively new to sequencing technology. Does anyone has a quick workflow with steps of how to analyze the data? I have some illumina exome sequence data. I know I need to align it first then do variance call. I want to know if there is anything else between alignment and snp call?

Thanks
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Old 06-13-2010, 10:26 PM   #2
Jose Blanca
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Hi:

We had mostly the same problem and we've developed a tool to automate that process. It is still in beta, but if you want to try it out, you'll be most than welcome.
You can find it here:
http://bioinf.comav.upv.es/ngs_backbone/
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Old 06-14-2010, 02:18 AM   #3
NGSfan
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Quote:
Originally Posted by foxyg View Post
Hi everyone, I am relatively new to sequencing technology. Does anyone has a quick workflow with steps of how to analyze the data? I have some illumina exome sequence data. I know I need to align it first then do variance call. I want to know if there is anything else between alignment and snp call?

Thanks
I would strongly suggest you have a careful study of the Genome Analysis Toolkit (GATK) from the Broad Institute. Be sure to look at the powerpoint slide they include. They give an example workflow and offer additional approaches to improving SNP/indel calling from quality score recalibration to local realignment of reads. I would highly recommend their approach since it cleans up a lot of the data.
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Old 06-14-2010, 02:20 AM   #4
NGSfan
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Quote:
Originally Posted by Jose Blanca View Post
Hi:

We had mostly the same problem and we've developed a tool to automate that process. It is still in beta, but if you want to try it out, you'll be most than welcome.
You can find it here:
http://bioinf.comav.upv.es/ngs_backbone/

This looks very interesting, thanks for sharing! I will have a look at it.
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