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, 13:35, 25 May 2010
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| --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded. | | --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded. |
| --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded. | | --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded. |
| + | |
| + | --hardFilter Filtered positions will be completely absent from output. The default is to use a soft filter, where these |
| + | positions are included in output but annotated as failing specific filters. |
| | | |
| === VCF Output === | | === VCF Output === |