Identifying SNPs: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
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. | 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. | ||
[[File:ExperimentView_findSNPs.png|thumb|right|500px|Find SNPs function highlighted in red]] | [[File:ExperimentView_findSNPs.png|thumb|right|500px|Find SNPs function (highlighted in red)]] | ||
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. | ||
| Line 13: | Line 13: | ||
We are working to incorporate other SNP-finding programs into CoGe. | We are working to incorporate other SNP-finding programs into CoGe. | ||
[[File:SNP_track.png|thumb|right|500px|Resulting SNP track (highlighted in red)]] | |||
Revision as of 18:46, 20 May 2014
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:
- 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.
