Identifying SNPs: Difference between revisions
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An alignment-type experiment in CoGe is created by loading a BAM file. See [[LoadExperiment]] for instruction on how to do this. | An alignment-type experiment in CoGe is created by loading a BAM file. See [[LoadExperiment]] for instruction on how to do this. | ||
The CoGe SNP finding pipeline detects SNPs that meet the following criteria: | The CoGe SNP finding pipeline detects SNPs that meet the following criteria (these values are configurable): | ||
* minimum read depth of 10 (of any base quality value) | * minimum read depth of 10 (of any base quality value) | ||
* minimum high-quality allele count of 4 (high quality is PHRED >= 20) | * minimum high-quality allele count of 4 (high quality is PHRED >= 20) | ||
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The SAMtools mpileup function is used to generate read depth counts for the BAM file. | The SAMtools mpileup function is used to generate read depth counts for the BAM file. | ||
We are working to incorporate other SNP-finding programs into CoGe. | We are working to incorporate other SNP-finding programs into CoGe. Let us know if you'd like your favorite tool added! | ||
[[File:SNP_track.png|thumb|right| | [[File:SNP_track.png|thumb|right|300px|Resulting SNP track (highlighted in red)]] | ||
Latest revision as of 16:52, 29 February 2016
CoGe has a built-in SNP finding pipeline! To find SNPs in an existing alignment-type experiment, select the "Find SNPs" analysis tool in the ExperimentView page.
An alignment-type experiment in CoGe is created by loading a BAM file. See LoadExperiment for instruction on how to do this.
The CoGe SNP finding pipeline detects SNPs that meet the following criteria (these values are configurable):
- minimum read depth of 10 (of any base quality value)
- minimum high-quality allele count of 4 (high quality is PHRED >= 20)
- minimum allele frequency of 10%.
The SAMtools mpileup function is used to generate read depth counts for the BAM file.
We are working to incorporate other SNP-finding programs into CoGe. Let us know if you'd like your favorite tool added!
