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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).
