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Old 09-20-2015, 09:24 PM   #1
JdevSEQnoob
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Location: Cali

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Default Help with SNP analysis

Hi, I'm new to the sequencing analysis. in the project that im working on, I have a list of SNP positions by chromosome, region and the reference allele call. However I have been retasked with annotating these SNPs back to a reference genome. Can anyone help direct me or help me get my path started? Thanks!

-JDev.
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Old 09-21-2015, 06:14 AM   #2
HESmith
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The simplest approach is to convert the data you have to VCF format, then use one of the annotation tools (e.g., ANNOVAR or snpEff). Be sure that you're using the same version of the reference used for the original SNP calls, or the results will be meaningless.
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Old 09-22-2015, 09:04 AM   #3
JdevSEQnoob
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ok, so I've got my SNPs annotated. now what is the best way to visualize this data. which program helps put all these points along a reference genome to look at?
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Old 09-22-2015, 09:25 AM   #4
GenoMax
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You should be able to use IGV or UCSC browser to visualize the tracks.
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