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@nvnieuwk
nvnieuwk committed Aug 9, 2024
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Expand Up @@ -66,7 +66,7 @@ Parameters that define how the pipeline works
| `automap_repeats` | BED file with repeat regions in the genome. <details><summary>Help</summary><small>This file will be automatically generated for hg38/GRCh38 and hg19/GRCh37 when this parameter has not been given.</small></details> | `string` | | | |
| `automap_panel` | TXT file with gene panel regions to be used by AutoMap. <details><summary>Help</summary><small>By default the CMGG gene panel list will be used.</small></details> | `string` | | | |
| `automap_panel_name` | The panel name of the panel given with --automap_panel. | `string` | cmgg_bio | | |
| `hc_phasing` | Perform phasing with HaplotypeCaller | `boolean` | | | |
| `hc_phasing` | Perform phasing with HaplotypeCaller | `boolean` | | | |

## Institutional config options

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