cli-find-snvs-help.txt

usage: WARNING this tool is experimental [-h] [--targets TARGETS]
                                         [--reference REFERENCE]
                                         [--bam BAM [BAM ...]] [--maf MAF]
                                         [--mad MAD] [--ind-maf IND_MAF]
                                         [--ind-mad IND_MAD]
                                         [--min-ind MIN_IND]
                                         [--read-group-field READ_GROUP_FIELD]
                                         [--mapping-quality MAPPING_QUALITY]
                                         [--keep-duplicate-reads]
                                         [--keep-qcfail-reads]
                                         [--keep-supplementary-reads]

options:
  -h, --help            show this help message and exit
  --targets TARGETS     Bed file containing genomic intervals. Basis SNVs will
                        only be identified from within these intervals. The
                        first three columns (contig, start, stop) are
                        mandatory.
  --reference REFERENCE
                        Indexed fasta file containing the reference genome.
  --bam BAM [BAM ...]   Bam file(s) to use in analysis. This may be (1) a list
                        of one or more bam filepaths, (2) a plain-text file
                        containing a single bam filepath on each line, (3) a
                        plain-text file containing a sample identifier and its
                        corresponding bam filepath on each line separated by a
                        tab. If options (1) or (2) are used then all samples
                        within each bam will be used within the analysis. If
                        option (3) is used then only the specified sample will
                        be extracted from each bam file and An error will be
                        raised if a sample is not found within its specified
                        bam file.
  --maf MAF             Minimum sample population allele frequency required to
                        include an allele (default = 0.0).
  --mad MAD             Minimum sample population allele depth required to
                        include an allele (default = 0).
  --ind-maf IND_MAF     Minimum allele frequency of an individual required to
                        include an allele (default = 0.1). Alleles will be
                        excluded if their frequency is lower than this value
                        across all samples.
  --ind-mad IND_MAD     Minimum allele depth of an individual required to
                        include an allele (default = 3). Alleles will be
                        excluded if their depth is lower than this value
                        across all samples.
  --min-ind MIN_IND     Minimum number of individuals required to meet the
                        --ind-maf and --ind-mad thresholds (default = 1).
  --read-group-field READ_GROUP_FIELD
                        Read group field to use as sample id (default = "SM").
                        The chosen field determines tha sample ids required in
                        other input files e.g. the --sample-list argument.
  --mapping-quality MAPPING_QUALITY
                        Minimum mapping quality of reads used in assembly
                        (default = 20).
  --keep-duplicate-reads
                        Flag: Use reads marked as duplicates in the assembly
                        (these are skipped by default).
  --keep-qcfail-reads   Flag: Use reads marked as qcfail in the assembly
                        (these are skipped by default).
  --keep-supplementary-reads
                        Flag: Use reads marked as supplementary in the
                        assembly (these are skipped by default).