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, 15:56, 15 October 2010
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| === total depth filter === | | === total depth filter === |
| For the 1000 Genomes Project (average depth per individual ~4X), we have found it useful to exclude sites with average total depth per individual < 0.5X or > 10X. | | For the 1000 Genomes Project (average depth per individual ~4X), we have found it useful to exclude sites with average total depth per individual < 0.5X or > 10X. |
| + | |
| + | === coverage filter === |
| + | We recommend the filter of >50% individuals with coverage. |
| + | |
| + | === flanking sequence filter === |
| + | We recommend excluding sites with >0.1% flanking 10-mer frequency among candidate sites. |
| + | |
| + | The rationale is .... |
| + | |
| + | === indel filter === |
| + | We recommend distance to known indels >= 5bp. |
| + | |
| + | === site promotion filter === |
| + | We recommend setting parameter -p at least >= 0.9 in step 1 (running glfMultiples). |