How to export novel SNP's

[Mat]

Once I get my Next Gen data into Savant is there a way to automatically parse the data and export all the SNP's that are novel (i.e do not appear in HapMap/1000genome data).

Also can I filter to show only SNP's that are present in a certain % of reads to eliminate false SNP calls.

Thanks

Mat

[Marc Fiume]

Hi Mat,

Also can I filter to show only SNP's that are present in a certain % of reads to eliminate false SNP calls.

Our SNP Finder plugin has a confidence threshold that you can adjust which allows you to filter out many false SNP calls.

Once I get my Next Gen data into Savant is there a way to automatically parse the data and export all the SNP's that are novel (i.e do not appear in HapMap/1000genome data).

You can use the SNP Finder to export a BED file (through the Bookmarks module) of all found SNPs. There is no built in functionality to annotate only novel SNPs, although this logic could easily be added as a separate plugin.

Hope that helps,

Marc

[Mat]

Hi Marc,

Thanks for the reply, I've tried installing the SNP Finder 2 plugin, but when I restart Savant I get the following error
"Unable to load plugin at /home/home/sp/.savant/plugins/savant.snp-2.1.0.jar
Please check if it is compatible with this version of Savant.
Uninstall it?"

I'm using Ubuntu if that helps.

Any ideas?

Mat

[Alessandro Guffanti]

I got the same error on WindowsXP Professional 64 bit and it seems impossible
to solve...

Thanks,

Alessandro

[Marc Fiume]

Hi Mat and Alessandro,

Thanks for reporting your issue. We've identified the problem and are working on the solution. I'll notify you when we have it fixed.

Take care,

Marc