Required parameters:
| Parameters | Type | Default | Description |
|---|---|---|---|
| --out_dir | PATH | None | output folder |
| --bam_fn | FILE | None | input bam file |
| --bed_fn | FILE | None | input target regions bed file |
| --ref_fn | FILE | None | input reference fasta |
Other parameters:
[EXPERIMENTAL] are for testing and advanced usage.
| Type | Parameters | Type | Default | Description |
|---|---|---|---|---|
| General options | --threads | INT | 48 | running threads, we recommend using 48 or above |
| - | --clair_ensemble_threads | INT | 16 | Clair-Ensemble threads, we recommend using 16 |
| - | --subtype_parallel | INT | 3 | [EXPERIMENTAL] number of subtypes parallel run Clair |
| initial filtering options | --indel_l | INT | 50 | filtering read with indel length > indel_l [50], set [0] to disable filtering |
| clusterV options | --top_k | INT | 25 | top k subtypes to output |
| - | --n_min_supports | INT | 50 | minimum read support for creating a subtype |
| - | --n_max_candidates | INT | 15 | [EXPERIMENTAL] number of selected candidates for clustering |
| - | --min_af | FLOAT | 0.05 | [EXPERIMENTAL] minimum AF when clustering |
| - | --n_max_coverage | INT | 10000 | [EXPERIMENTAL] maximum read for clustering |
| consensus and HIVDB report options | --hivdb_url | STR | "" | hivdb URL default query from the internet, for localizing the HIVDB, please check https://github.com/hivdb/sierra, and update this setting accordingly, e.g. using --hivdb_url http://localhost:8111/sierra/rest/graphql |
| - | --n_of_read_for_consensus | INT | 1000 | [EXPERIMENTAL] number of original read for generating consensus |
| - | --flye_genome_size | STR | 5k | [EXPERIMEANTAL], flye --genome-size for generating consensus, we recommend using 5k for HIV genome |
| - | --flye_nano_type | STR | nano-hq | [EXPERIMEANTAL], flye option for different ONT type, default --nano-hq, check https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md |