Command-Line Help for clam
This page contains the help content for the clam command-line program.
Command Overview:
clam
Usage: clam [OPTIONS] <COMMAND>
Commands:
loci Calculate callable sites from depth statistics.
stat Calculate population genetic statistics from VCF using callable sites.
help Print this message or the help of the given subcommand(s)
Options:
-v, --verbose... Increase verbosity (-v, -vv for more verbosity)
-q, --quiet Suppress output (overrides verbosity)
-h, --help Print help
-V, --version Print version
clam loci
Usage: clam loci [OPTIONS] -o <OUTDIR> [INPUT]...
Arguments:
[INPUT]... Input files (D4 format by default). Specify one or more files directly
Options:
-f, --filelist <FILELIST> Path to file containing list of input files, one per line. Use this instead of positional input arguments for many files
--gvcf Use GVCF format instead of default D4 format for input files
--merged Input is a merged D4 file (single file containing multiple samples)
-o <OUTDIR> Output directory for results (required)
--bed Write additional BED file. Note: This can be slow for large datasets
-h, --help Print help
-V, --version Print version
Sample-level Thresholds:
-m, --min-depth <MIN_DEPTH>
Minimum depth to consider a site callable for each individual [default: 0]
-M, --max-depth <MAX_DEPTH>
Maximum depth to consider a site callable for each individual [default: inf]
--thresholds-file <THRESHOLD_FILE>
Custom thresholds per chromosome. Tab-separated file: chrom, min, max
Population-level Thresholds:
-d, --depth-proportion <DEPTH_PROPORTION>
Proportion of samples that must pass thresholds at a site to consider it callable. Value between 0.0 and 1.0 [default: 0]
-u, --min-mean-depth <MEAN_DEPTH_MIN>
Minimum mean depth across all samples required at a site to consider it callable [default: 0]
-U, --max-mean-depth <MEAN_DEPTH_MAX>
Maximum mean depth across all samples allowed at a site to consider it callable [default: inf]
-p, --population-file <POPULATION_FILE>
Path to file that defines populations. Tab separated: sample, population_name
Chromosome Filtering:
-x <EXCLUDE>... Comma separated list of chromosomes to exclude. Example: --exclude chr1,chr2,chrX
--exclude-file <EXCLUDE_FILE> Path to file with chromosomes to exclude, one per line
-i <INCLUDE>... Comma separated list of chromosomes to include (restrict analysis to). Example: --include chr1,chr2,chr3
--include-file <INCLUDE_FILE> Path to file with chromosomes to include, one per line
Performance:
-t, --threads <THREADS> Number of threads to use for parallel processing [default: 1]
EXAMPLES:
# Basic usage with positional input files
clam loci -o output_dir input1.d4 input2.d4
# Using a file list instead of positional arguments
clam loci -f filelist.txt -o output_dir
# Set custom depth thresholds
clam loci -o output_dir -m 10 -M 100 input1.d4 input2.d4
clam stat
Usage: clam stat [OPTIONS] <--window-size <WINDOW_SIZE>|--regions-file <REGIONS_FILE>> <VCF> [CALLABLE_SITES]
Arguments:
<VCF> Path to input VCF file
[CALLABLE_SITES] Path to input callable sites D4 file from clam loci
Options:
-o, --outdir <OUTDIR>
Where to write output files. Defaults to current working directory
-t, --threads <THREADS>
Number of threads to use [default: 1]
-w, --window-size <WINDOW_SIZE>
Size of windows for statistics in bp. Conflicts with 'regions-file'
-r, --regions-file <REGIONS_FILE>
File specifying regions to calculate statistics for. Conflicts with 'window-size'
-s, --sites-file <SITES_FILE>
Specify sites to consider for calculations. Bed format
-p, --population-file <POPULATION_FILE>
Path to file that defines populations. Tab separated: sample, population_name
-f, --fai <FASTA_INDEX>
Path to fasta index for reference VCF was called against. Only needed if VCF does not have contig info in the header
-x <EXCLUDE>...
Comma separated list of chromosomes to exclude
--exclude-file <EXCLUDE_FILE>
Path to file with chromosomes to exclude, one per line
--roh-file <ROH_FILE>
Path to RoH file
-i <INCLUDE>...
Comma separated list of chromosomes to include (restrict analysis to)
--include-file <INCLUDE_FILE>
Path to file with chromosomes to include, one per line
-h, --help
Print help