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Old 09-18-2012, 03:29 PM   #1
DFJ111
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Location: Auckland

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Thumbs up SNP calling vs. individual curated genes using 454 data from multiple heterozygotes

Hi.. yes, the title says it all. I need to identify novel SNPs (or, for that matter, any polymorphisms) in a bunch of curated genes (1500 or so). We don't have a genome. I have a lot of 454 exome sequencing data, which is specifically enriched for the genes I am looking at; this comes from a number of individuals in a mapping population.

So far, I have de novo assembled the 454 data (to ensure that the gene models we have are valid, but that's a different problem). I've also had a go at mapping the raw 454 reads (from one individual) using an individual gene as a backbone. Obvious SNPs there. This has been done using both MIRA and Geneious. MIRA produces a file detailing where it thinks there are SNPs, but I don't want to re-invent the wheel by writing a program to convert it into a .gff file if it's been done already, and there's no statistical "niceness" score for the SNPs.

So a few questions..
1)Is there any software that can call SNPs/polymorphisms and give me some statistical measure of the "goodness" of the SNP, i.e. the likelihood that the SNP is correct and not just a sequencing artefact?
2) Is there any software that can call SNPs and produce an annotation track ( .gff file) that I can then annotate the gene models with?
3) Is the above a good approach and am I missing anything?

Any tips on automating this process would be appreciated too. I've already written scripts to automate the de novo assembly / mapping to individual genes, but tips on how to select good SNPs from the mapping etc would be nice.

Thanks all from New Zealand!
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Old 11-17-2012, 08:49 PM   #2
seq4freedom
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Start with Galaxy... I'll give it some research and get back to you!
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Old 11-18-2012, 04:19 AM   #3
JackieBadger
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Well the quality of your SNP can be determined by the depth you require, the SNP base quality score, and the quality of neighboring bases. All of these you can set...Im pretty sure in mira.
There are plenty of SNP programs that use bayesian stats to call SNPs: http://www.biostars.org/p/5395/
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