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Update parameters.md
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fellen31 authored Sep 23, 2024
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Expand Up @@ -97,7 +97,7 @@ Workflow options specific to genomic-medicine-sweden/nallo
| `preset` | Enable or disable certain parts of the pipeline by default, depending on data type (`revio`, `pacbio`, `ONT_R10`) | `string` | revio | True | |
| `variant_caller` | Which short variant software to use (`deepvariant`) | `string` | deepvariant | | |
| `sv_caller` | Which structural variant caller to use (`severus`, `sniffles`) | `string` | severus | | |
| `phaser` | Which phasing software to use (`longphase`, `whatshap`, `hiphase`) | `string` | longphase_snv | | |
| `phaser` | Which phasing software to use (`longphase`, `whatshap`, `hiphase`) | `string` | longphase | | |
| `hifiasm_mode` | Run hifiasm in hifi-only or hifi-trio mode (`hifi-only`, `trio-binning`) | `string` | hifi-only | | |
| `parallel_alignments` | If parallel_alignments is bigger than 1, input files will be split and aligned in parallel to reduce processing time. | `integer` | 1 | | |
| `parallel_snv` | If parallel_snv is bigger than 1, short variant calling will be done in parallel to reduce processing time. | `integer` | 13 | | |
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