`--input-dir` | `input_dir_path` | Path to a folder containing demultiplexed reads |
`--output-file`| `output_file_path`| Path to the output file |
`--threads`| `n_threads`| Number of threads to use (default: 1) |
`--min-coverage`| `min_cov`| Minimum coverage to consider a sequence in an individual (default: 1) |
Option | Description
--- | ---
`--input-dir` | Path to a folder containing demultiplexed reads |
`--output-file` | Path to the output file |
`--threads` | Number of threads to use (default: 1) |
`--min-coverage` | Minimum coverage to consider a sequence in an individual (default: 1) |
### distrib
...
...
@@ -148,13 +148,13 @@ Option | Full name | Description
**Options** :
Option | Full name | Description
------ | --------- | -------------
`--input-file` | `input_file_path` | Path to an coverage table obtained with `process` |
`--output-file`| `output_file_path`| Path to the output file |
`--popmap-file`| `popmap_file_path`| Path to a popmap file indicating the sex of each individual |
`--min-coverage`| `min_cov`| Minimum coverage to consider a sequence present in an individual (default: 1) |
`--output-matrix`| `output_matrix`| If true, outputs the resutls as a matrix with males in columns and females in rows instead of a table (default: false) |
Option | Description
------ | -------------
`--input-file` | Path to an coverage table obtained with `process` |
`--output-file` | Path to the output file |
`--popmap-file` | Path to a popmap file indicating the sex of each individual |
`--min-coverage` | Minimum coverage to consider a sequence present in an individual (default: 1) |
`--output-matrix` | If true, outputs the resutls as a matrix with males in columns and females in rows instead of a table (default: false) |
### subset
...
...
@@ -164,19 +164,19 @@ Option | Full name | Description
**Options** :
Option | Full name | Description
--- | --- | ---
`--input-file` | `input_file_path` | Path to an coverage table obtained with `process` |
`--output-file`| `output_file_path`| Path to the output file |
`--popmap-file`| `popmap_file_path`| Path to a popmap file indicating the sex of each individual |
`--output-format`| `output-format`| Output format, either "table" or "fasta" |
`--min-coverage`| `min_cov`| Minimum coverage to consider a sequence present in an individual (default: 1) |
`--min-males`| `min_males`| Minimum number of males with a retained sequence |
`--min-females`| `min_females`| Minimum number of females with a retained sequence |
`--max-males`| `max_males`| Maximum number of males with a retained sequence |
`--max-females`| `max_females`| Maximum number of females with a retained sequence |
`--max-individuals`| `max_individuals`| Maximum number of individuals with a retained sequence |
`--max-individuals`| `max_individuals`| Maximum number of individuals with a retained sequence |
Option | Description
--- | ---
`--input-file` | Path to an coverage table obtained with `process` |
`--output-file` | Path to the output file |
`--popmap-file` | Path to a popmap file indicating the sex of each individual |
`--output-format` | Output format, either "table" or "fasta" |
`--min-coverage` | Minimum coverage to consider a sequence present in an individual (default: 1) |
`--min-males` | Minimum number of males with a retained sequence |
`--min-females` | Minimum number of females with a retained sequence |
`--max-males` | Maximum number of males with a retained sequence |
`--max-females` | Maximum number of females with a retained sequence |
`--max-individuals` | Maximum number of individuals with a retained sequence |
`--max-individuals` | Maximum number of individuals with a retained sequence |
### signif
...
...
@@ -186,13 +186,13 @@ Option | Full name | Description
**Options** :
Option | Full name | Description
--- | --- | ---
`--input-file` | `input_file_path` | Path to an coverage table obtained with `process` |
`--output-file`| `output_file_path`| Path to the output file |
`--popmap-file`| `popmap_file_path`| Path to a popmap file indicating the sex of each individual |
`--output-format`| `output-format`| Output format, either "table" or "fasta" |
`--min-coverage`| `min_cov`| Minimum coverage to consider a sequence present in an individual (default: 1) |
Option | Description
--- | ---
`--input-file` | Path to an coverage table obtained with `process` |
`--output-file` | Path to the output file |
`--popmap-file` | Path to a popmap file indicating the sex of each individual |
`--output-format` | Output format, either "table" or "fasta" |
`--min-coverage` | Minimum coverage to consider a sequence present in an individual (default: 1) |
### map
...
...
@@ -202,15 +202,15 @@ Option | Full name | Description
**Options** :
Option | Full name | Description
--- | --- | ---
`--input-file` | `input_file_path` | Path to an coverage table obtained with `process` |
`--output-file`| `output_file_path`| Path to the output file |
`--popmap-file`| `popmap_file_path`| Path to a popmap file indicating the sex of each individual |
`--genome-file`| `genome_file_path`| Path to a reference genome file in fasta format |
`--min-coverage`| `min_cov`| Minimum coverage to consider a sequence present in an individual (default: 1) |
`--min-quality`| `min_quality`| Minimum mapping quality, as defined in BWA, to consider a sequence properly mapped (default: 20) |
`--min-frequency`| `min_frequency`| Minimum frequency in at least one sex for a sequence to be retained (default: 0.25) |
Option | Description
--- | ---
`--input-file` | Path to an coverage table obtained with `process` |
`--output-file` | Path to the output file |
`--popmap-file` | Path to a popmap file indicating the sex of each individual |
`--genome-file` | Path to a reference genome file in fasta format |
`--min-coverage` | Minimum coverage to consider a sequence present in an individual (default: 1) |
`--min-quality` | Minimum mapping quality, as defined in BWA, to consider a sequence properly mapped (default: 20) |
`--min-frequency` | Minimum frequency in at least one sex for a sequence to be retained (default: 0.25) |
### freq
...
...
@@ -220,11 +220,11 @@ Option | Full name | Description
**Options** :
Option | Full name | Description
--- | --- | ---
`--input-file` | `input_file_path` | Path to an coverage table obtained with `process` |
`--output-file`| `output_file_path`| Path to the output file |
`--min-coverage`| `min_cov`| Minimum coverage to consider a sequence present in an individual (default: 1) |
Option | Description
--- | ---
`--input-file` | Path to an coverage table obtained with `process` |
`--output-file` | Path to the output file |
`--min-coverage` | Minimum coverage to consider a sequence present in an individual (default: 1) |
