cgatools version 1.2.0 build 11
usage: cgatools COMMAND [ options ] [ positionalArgs ]

For help on a particular command CMD, try "cgatools help CMD".
Available commands:
    help          Prints help information.
    man           Prints the cgatools reference manual.
    fasta2crr     Converts fasta reference files to the crr format.
    crr2fasta     Converts a crr reference file to the fasta format.
    listcrr       Lists chromosomes, contigs, or ambiguous sequences of a crr 
                  file.
    decodecrr     Prints the reference sequence for a given reference range.
    snpdiff       Compares snp calls to a Complete Genomics variant file.
    calldiff      Compares two Complete Genomics variant files.
    listvariants  Lists the variants present in a variant file.
    testvariants  Tests variant files for presence of variants.
    map2sam       Converts CGI initial reference mappings into SAM format.
    evidence2sam  Converts CGI variant evidence data into SAM format.
    join          Joins two tab-delimited files based on equal fields or 
                  overlapping regions.
    junctiondiff  Reports difference between junction calls of Complete 
                  Genomics junctions files.
    


-------------------------------------------------------------------------------

COMMAND NAME
    help - Prints help information.

OPTIONS
  -h [ --help ] 
        Print this help message.

  --command arg
        The command to describe.

  --format arg (=text)
        The format of the output stream (text or html).

  --output arg (=STDOUT)
        The output file (may be omitted for stdout).




-------------------------------------------------------------------------------

COMMAND NAME
    man - Prints the cgatools reference manual.

OPTIONS
  -h [ --help ] 
        Print this help message.

  --output arg (=STDOUT)
        The output file (may be omitted for stdout).

  --format arg (=text)
        The format of the output stream (text or html).




-------------------------------------------------------------------------------

COMMAND NAME
    fasta2crr - Converts fasta reference files to the crr format.

OPTIONS
  -h [ --help ] 
        Print this help message.

  --input arg
        The input fasta files (may be positional args, or omitted for stdin). 
        Take care to specify the fasta files in chromosome order; ordering is 
        important. To work with human Complete Genomics data, the chromosome 
        order should be chr1...chr22, chrX, chrY, chrM.

  --output arg
        The output crr file.

  --circular arg
        A comma-separated list of circular chromosome names. If ommitted, 
        defaults to chrM.




-------------------------------------------------------------------------------

COMMAND NAME
    crr2fasta - Converts a crr reference file to the fasta format.

OPTIONS
  -h [ --help ] 
        Print this help message.

  --input arg
        The input crr file (may be positional arg).

  --output arg (=STDOUT)
        The output fasta file (may be omitted for stdout).

  --line-width arg (=50)
        The maximum width of a line of sequence.




-------------------------------------------------------------------------------

COMMAND NAME
    listcrr - Lists chromosomes, contigs, or ambiguous sequences of a crr file.

DESCRIPTION
    For mode=chromosome, prints a space-separated table describing each 
    chromosome within the reference. The columns are defined as follows:
    
        ChromosomeId A numeric identifier for the chromosome.
        Chromosome   The name of the chromosome.
        Length       The length in bases of the chromosome.
        Circular     Boolean indicating if the chromosome is circular.
        Md5          Md5 of the string containing the upper case IUPAC code for
                     each base in the chromosome (spaces and dashes are 
                     omitted).
    
    For mode=contig, prints a space-separated table describing each gap and 
    each contig within the reference. Here, a gap between contigs is defined as
    any stretch of min-contig-gap-length or more no-called reference bases (N 
    character). The columns are defined as follows:
    
        ChromosomeId A numeric identifier for the chromosome.
        Chromosome   The name of the chromosome.
        Type         Either CONTIG or GAP.
        Offset       The 0-based offset of the start of the contig or gap 
                     within the chromosome.
        Length       The length in bases of the contig or gap.
    
    For mode=ambiguity, prints a space-separated table describing each run of 
    ambiguity codes within the reference. The columns are defined as follows:
    
        ChromosomeId A numeric identifier for the chromosome.
        Chromosome   The name of the chromosome.
        Code         The IUPAC code for the region.
        Offset       The 0-based offset of the run of ambiguity codes in the 
                     chromosome.
        Length       The length in bases of the run of ambiguity codes.

OPTIONS
  -h [ --help ] 
        Print this help message.

  --reference arg
        The reference crr file (may be positional arg).

  --output arg (=STDOUT)
        The output file (may be omitted for stdout).

  --mode arg (=chromosome)
        One of chromosome, contig, or ambiguity.

  --min-contig-gap-length arg (=50)
        Minimum length of gap between reference contigs, for mode=contig.




-------------------------------------------------------------------------------

COMMAND NAME
    decodecrr - Prints the reference sequence for a given reference range.

OPTIONS
  -h [ --help ] 
        Print this help message.

  --reference arg
        The reference crr file (may be positional arg).

  --output arg (=STDOUT)
        The output file (may be omitted for stdout).

  --range arg
        The range of bases to print (chr,begin,end or chr:begin-end).




-------------------------------------------------------------------------------

COMMAND NAME
    snpdiff - Compares snp calls to a Complete Genomics variant file.

DESCRIPTION
    Compares the snp calls in the "genotypes" file to the calls in a Complete 
    Genomics variant file. The genotypes file is a tab-delimited file with at 
    least the following columns (additional columns may be given):
    
        Chromosome      (Required) The name of the chromosome.
        Offset0Based    (Required) The 0-based offset in the chromosome.
        GenotypesStrand (Optional) The strand of the calls in the Genotypes 
                        column (+ or -, defaults to +).
        Genotypes       (Optional) The calls, one per allele. The following 
                        calls are recognized:
                        A,C,G,T A called base.
                        N       A no-call.
                        -       A deleted base.
                        .       A non-snp variation.
    
    The output is a tab-delimited file consisting of the columns of the 
    original genotypes file, plus the following additional columns:
    
        Reference         The reference base at the given position.
        VariantFile       The calls made by the variant file, one per allele. 
                          The character codes are the same as is described for 
                          the Genotypes column.
        DiscordantAlleles (Only if Genotypes is present) The number of 
                          Genotypes alleles that are discordant with calls in 
                          the VariantFile. If the VariantFile is described as 
                          haploid at the given position but the Genotypes is 
                          diploid, then each genotype allele is compared 
                          against the haploid call of the VariantFile.
        NoCallAlleles     (Only if Genotypes is present) The number of 
                          Genotypes alleles that were no-called by the 
                          VariantFile. If the VariantFile is described as 
                          haploid at the given position but the Genotypes is 
                          diploid, then a VariantFile no-call is counted twice.
    
    The verbose output is a tab-delimited file consisting of the columns of the
    original genotypes file, plus the following additional columns:
    
        Reference   The reference base at the given position.
        VariantFile The call made by the variant file for one allele (there is 
                    a line in this file for each allele). The character codes 
                    are the same as is described for the Genotypes column.
        [CALLS]     The rest of the columns are pasted in from the VariantFile,
                    describing the variant file line used to make the call.
    
    The stats output is a comma-separated file with several tables describing 
    the results of the snp comparison, for each diploid genotype. The tables 
    all describe the comparison result (column headers) versus the genotype 
    classification (row labels) in different ways. The "Locus classification" 
    tables have the most detailed match classifications, while the "Locus 
    concordance" tables roll these match classifications up into "discordance" 
    and "no-call". A locus is considered discordant if it is discordant for 
    either allele. A locus is considered no-call if it is concordant for both 
    alleles but has a no-call on either allele. The "Allele concordance" 
    describes the comparison result on a per-allele basis.

OPTIONS
  -h [ --help ] 
        Print this help message.

  --reference arg
        The input crr file.

  --variants arg
        The input variant file.

  --genotypes arg
        The input genotypes file.

  --output-prefix arg
        The path prefix for all output reports.

  --reports arg (=Output,Verbose,Stats)
        Comma-separated list of reports to generate. A report is one of:
            Output  The output genotypes file.
            Verbose The verbose output file.
            Stats   The stats output file.
        


SUPPORTED FORMAT_VERSION
    0.3 or later



-------------------------------------------------------------------------------

COMMAND NAME
    calldiff - Compares two Complete Genomics variant files.

DESCRIPTION
    Compares two Complete Genomics variant files. Divides the genome up into 
    superloci of nearby variants, then compares the superloci. Also refines the
    comparison to determine per-call or per-locus comparison results.
    
    Comparison results are usually described by a semi-colon separated string, 
    one per allele. Each allele's comparison result is one of the following 
    classifications:
    
        ref-identical   The alleles of the two variant files are identical, and
                        they are consistent with the reference.
        alt-identical   The alleles of the two variant files are identical, and
                        they are inconsistent with the reference.
        ref-consistent  The alleles of the two variant files are consistent, 
                        and they are consistent with the reference.
        alt-consistent  The alleles of the two variant files are consistent, 
                        and they are inconsistent with the reference.
        onlyA           The alleles of the two variant files are inconsistent, 
                        and only file A is inconsistent with the reference.
        onlyB           The alleles of the two variant files are inconsistent, 
                        and only file B is inconsistent with the reference.
        mismatch        The alleles of the two variant files are inconsistent, 
                        and they are both inconsistent with the reference.
        phase-mismatch  The two variant files would be consistent if the 
                        hapLink field had been empty, but they are 
                        inconsistent.
        ploidy-mismatch The superlocus did not have uniform ploidy.
    
    In some contexts, this classification is rolled up into a simplified 
    classification, which is one of "identical", "consistent", "onlyA", 
    "onlyB", or "mismatch".
    
    A good place to start looking at the results is the superlocus-output file.
    It has columns defined as follows:
    
        SuperlocusId   An identifier given to the superlocus.
        Chromosome     The name of the chromosome.
        Begin          The 0-based offset of the start of the superlocus.
        End            The 0-based offset of the base one past the end of the 
                       superlocus.
        Classification The match classification of the superlocus.
        Reference      The reference sequence.
        AllelesA       A semicolon-separated list of the alleles (one per 
                       haplotype) for variant file A, for the phasing with the 
                       best comparison result.
        AllelesB       A semicolon-separated list of the alleles (one per 
                       haplotype) for variant file B, for the phasing with the 
                       best comparison result.
    
    The locus-output file contains, for each locus in file A and file B that is
    not consistent with the reference, an annotated set of calls for the locus.
    The calls are annotated with the following columns:
    
        SuperlocusId            The id of the superlocus containing the locus.
        File                    The variant file (A or B).
        LocusClassification     The locus classification is determined by the 
                                varType column of the call that is inconsistent
                                with the reference, concatenated with a 
                                modifier that describes whether the locus is 
                                heterozygous, homozygous, or contains no-calls.
                                If there is no one variant in the locus (i.e., 
                                it is heterozygous alt-alt), the locus 
                                classification begins with "other".
        LocusDiffClassification The match classification for the locus. This is
                                defined to be the best of the comparison of the
                                locus to the same region in the other file, or 
                                the comparison of the superlocus.
    
    The somatic output file contains a list of putative somatic variations of 
    genome A. The output includes only those loci that can be classified as 
    heterozygous or homozygous snp, del, ins or sub in file A, and are called 
    reference in the file B. Every locus is annotated with the following 
    columns:
    
        VarScoreA               The alternative score of the variation in 
                                genome A; this is the reference score for SNPs,
                                and the evidence score for other variations.
        RefScoreB               Minimum of the reference scores of the locus in
                                genome B.
        SomaticScore            The score that indicates the likelihood that 
                                the listed varition is indeed somatic, as 
                                opposed to a false negative in genome B or a 
                                false positive in the genome A.
    
    Superlocus comparison statistics can be found in the superlocus-stats file.
    Locus comparison statistics can be found in the locus-stats file. Beware 
    any output files whose parameter name begins with "debug".

OPTIONS
  -h [ --help ] 
        Print this help message.

  --reference arg
        The input crr file.

  --variantsA arg
        The "A" input variant file.

  --variantsB arg
        The "B" input variant file.

  --output-prefix arg
        The path prefix for all output reports.

  --reports arg (=SuperlocusOutput,SuperlocusStats,LocusOutput,LocusStats)
        Comma-separated list of reports to generate. A report is one of:
            SuperlocusOutput      Report for superlocus classification.
            SuperlocusStats       Report for superlocus classification stats.
            LocusOutput           Report for locus classification.
            LocusStats            Report for locus stats.
            SomaticOutput         Report for the list of simple variations that
                                  are present only in file "A", annotated with 
                                  the score that indicates the probability of 
                                  the variation being truly somatic. Requires 
                                  beta, export-rootA, and export-rootB options 
                                  to be provided as well. Note: generating this
                                  report slows calldiff by 10x-20x.
            DebugCallOutput       Report for call classification.
            DebugSuperlocusOutput Report for debug superlocus information.
            DebugSomaticOutput    Report for distribution estimates used for 
                                  somatic rescoring. Only produced if 
                                  SomaticOutput is also turned on.
        

  --locus-stats-column-count arg (=15)
        The number of columns for locus compare classification in the locus 
        stats file.

  --max-hypothesis-count arg (=32)
        The maximum number of possible phasings to consider for a superlocus.

  --no-reference-cover-validation 
        Turns off validation that all bases of a chromosome are covered by 
        calls of the variant file.

  --export-rootA arg
        The "A" export package root, for example /data/GS00118-DNA_A01; this 
        directory is expected to contain ASM/REF and ASM/EVIDENCE 
        subdirectories.

  --export-rootB arg
        The "B" export package root.

  --beta 
        This flag enables the SomaticOutput report, which is beta 
        functionality.


SUPPORTED FORMAT_VERSION
    0.3 or later



-------------------------------------------------------------------------------

COMMAND NAME
    listvariants - Lists the variants present in a variant file.

DESCRIPTION
    Lists all called variants present in the specified variant files, in a 
    format suitable for processing by the testvariants command. The output is a
    tab-delimited file consisting of the following columns:
    
        variantId  Sequential id assigned to each variant.
        chromosome The chromosome of the variant.
        begin      0-based reference offset of the beginning of the variant.
        end        0-based reference offset of the end of the variant.
        varType    The varType as extracted from the variant file.
        reference  The reference sequence.
        alleleSeq  The variant allele sequence as extracted from the variant 
                   file.
        xRef       The xRef as extrated from the variant file.

OPTIONS
  -h [ --help ] 
        Print this help message.

  --beta 
        This is a beta command. To run this command, you must pass the --beta 
        flag.

  --reference arg
        The reference crr file.

  --output arg (=STDOUT)
        The output file (may be omitted for stdout).

  --variants arg
        The input variant files (may be positional args).

  --variant-listing arg
        The output of another listvariants run, to be merged in to produce the 
        output of this run.

  --list-long-variants 
        In addition to listing short variants, list longer variants as well 
        (10's of bases) by concatenating nearby calls.
        


SUPPORTED FORMAT_VERSION
    0.3 or later



-------------------------------------------------------------------------------

COMMAND NAME
    testvariants - Tests variant files for presence of variants.

DESCRIPTION
    Tests variant files for presence of variants. The output is a tab-delimited
    file consisting of the columns of the input variants file, plus a column 
    for each assembly results file that contains a character code for each 
    allele. The character codes have meaning as follows:
    
        0 This allele of this genome is consistent with the reference at this 
          locus but inconsistent with the variant.
        1 This allele of this genome has the input variant at this locus.
        N This allele of this genome has no-calls but is consistent with the 
          input variant.
    

OPTIONS
  -h [ --help ] 
        Print this help message.

  --beta 
        This is a beta command. To run this command, you must pass the --beta 
        flag.

  --reference arg
        The reference crr file.

  --input arg (=STDIN)
        The input variants to test for.

  --output arg (=STDOUT)
        The output file (may be omitted for stdout).

  --variants arg
        The input variant files (may be positional args).


SUPPORTED FORMAT_VERSION
    0.3 or later



-------------------------------------------------------------------------------

COMMAND NAME
    map2sam - Converts CGI initial reference mappings into SAM format.

DESCRIPTION
    The Map2Sam converter takes as input Reads and Mappings files, a library 
    structure file and a crr reference file and generates one SAM file as an 
    output. The output is sent into stdout by default. All the mapping records 
    from the input are converted into corresponding SAM records one to one. In 
    addition, the unmapped DNB records are reported as SAM records having 
    appropriate indication. Map2Sam converter tries to identify primary 
    mappings and highlight them using the appropriate flag. The negative gaps 
    in CGI mappings are represented using GS/GQ/GC tags.

OPTIONS
  -h [ --help ] 
        Print this help message.

  -r [ --reads ] arg
        Input reads file.

  -m [ --mappings ] arg
        Input mappings file.

  -l [ --library ] arg
        Input library file.

  -s [ --reference ] arg
        Reference file.

  -o [ --output ] arg (=STDOUT)
        The output SAM file (may be omitted for stdout).

  -f [ --from ] arg (=0)
        Defines start read record of the export range.

  -t [ --to ] arg (=18446744073709551615)
        Defines end read record of the export range (the end record is not 
        exported).

  -e [ --export-region ] arg
        defines an export region as a half-open interval 'chr,from,to'

  --skip-not-mapped 
        Skip not mapped records

  --add-mate-sequence 
        Generate mate sequence and score tags.

  --mate-sv-candidates 
        Inconsistent mappings are normally converted as single arm mappings 
        with no mate information provided. If the option is used map2sam will 
        mate unique single arm mappings in SAM including those on different 
        stands and chromosomes. To distinguish these "artificially" mated 
        records a tag "XS:i:1" is used. The MAPQ provided for these records is 
        a single arm mapping weight.


SUPPORTED FORMAT_VERSION
    0.3 or later



-------------------------------------------------------------------------------

COMMAND NAME
    evidence2sam - Converts CGI variant evidence data into SAM format.

DESCRIPTION
    The evidence2sam converter takes as input evidence mapping files 
    (evidenceDnbs-*) and generates one SAM file as an output. The output is 
    sent into stdout by default. All the evidence mapping records from the 
    input are converted into a pair of corresponding SAM records - one record 
    for each HalfDNB. Evidence2Sam converter reports all mappings as not 
    primary. The negative gaps in CGI mappings are represented using GS/GQ/GC 
    tags.

OPTIONS
  -h [ --help ] 
        Print this help message.

  --beta 
        This is a beta command. To run this command, you must pass the --beta 
        flag.

  -e [ --evidence-dnbs ] arg
        Input evidence dnbs file.

  -s [ --reference ] arg
        Reference file.

  -o [ --output ] arg (=STDOUT)
        The output SAM file (may be omitted for stdout).

  -r [ --export-region ] arg
        defines an export region as a half-open interval 'chr,from,to'.

  --keep-duplicates 
        Keep local duplicates of DNB mappings.All the output SAM records will 
        be marked as not primary if this option is used.

  --add-mate-sequence 
        Generate mate sequence and score tags.

  --add-allele-id 
        Generate interval id and allele id tags.

  -v [ --debug-output ] 
        Generate verbose debug output. Please don't rely on this option in 
        production.


SUPPORTED FORMAT_VERSION
    0.3 or later



-------------------------------------------------------------------------------

COMMAND NAME
    join - Joins two tab-delimited files based on equal fields or overlapping regions.

DESCRIPTION
    Joins two tab-delimited files based on equal fields or overlapping regions.
    By default, an output record is produced for each match found between file 
    A and file B, but output format can be controlled by the --output-mode 
    parameter.

OPTIONS
  -h [ --help ] 
        Print this help message.

  --beta 
        This is a beta command. To run this command, you must pass the --beta 
        flag.

  --input arg
        File name to use as input (may be positional args, or omitted for 
        stdin). There must be exactly two input files to join. If only one file
        is specified by name, file A is taken to be stdin and file B is the 
        named file. File B is read fully into memory, and file A is streamed. 
        File A's columns appear first in the output.

  --output arg (=STDOUT)
        The output file name (may be omitted for stdout).

  --match arg
        A match specification, which is a column from A and a column from B 
        separated by a colon.

  --overlap arg
        Overlap specification. An overlap specification consists of a range 
        definition for files A and B, separated by a colon. A range definition 
        may be two columns, in which case they are interpreted as the beginning
        and end of the range. Or it may be one column, in which case the range 
        is defined as the 1-base range starting at the given value. The records
        from the two files must overlap in order to be considered for output. 
        Two ranges are considered to overlap if the overlap is at least one 
        base long, or if one of the ranges is length 0 and the ranges overlap 
        or abut. For example, "begin,end:offset" will match wherever end-begin 
        > 0, begin<offset+1, and end>offset, or wherever end-begin = 0, 
        begin<=offset+1, and end>=offset.

  -m [ --output-mode ] arg (=full)
        Output mode, one of the following:
            full        Print an output record for each match found between 
                        file A and file B.
            compact     Print at most one record for each record of file A, 
                        joining the file B values by a semicolon and 
                        suppressing repeated B values and empty B values.
            compact-pct Same as compact, but for each distinct B value, 
                        annotate with the percentage of the A record that is 
                        overlapped by B records with that B value. Percentage 
                        is rounded up to nearest integer.

  --overlap-mode arg (=strict)
        Overlap mode, one of the following:
            strict                Range A and B overlap if A.begin < B.end and 
                                  B.begin < A.end.
            allow-abutting-points Range A and B overlap they meet the strict 
                                  requirements, or if A.begin <= B.end and 
                                  B.begin <= A.end and either A or B has zero 
                                  length.

  --select arg (=A.*,B.*)
        Set of fields to select for output.

  -a [ --always-dump ] 
        Dump every record of A, even if there are no matches with file B.

  --overlap-fraction-A arg (=0)
        Minimum fraction of A region overlap for filtering output.

  --boundary-uncertainty-A arg (=0)
        Boundary uncertainty for overlap filtering. Specifically, records 
        failing the following predicate are filtered away: overlap >= 
        overlap-fraction-A * ( A-range-length - boundary-uncertainty-A )

  --overlap-fraction-B arg (=0)
        Minimum fraction of B region overlap for filtering output.

  --boundary-uncertainty-B arg (=0)
        Boundary uncertainty for overlap filtering. Specifically, records 
        failing the following predicate are filtered away: overlap >= 
        overlap-fraction-B * ( B-range-length - boundary-uncertainty-B )


SUPPORTED FORMAT_VERSION
    Any



-------------------------------------------------------------------------------

COMMAND NAME
    junctiondiff - Reports difference between junction calls of Complete Genomics junctions files.

DESCRIPTION
    junctiondiff takes two junction files A and B as input and produces the 
    following output:
      - "diff-inputFileName" - the junctions from an input file A that are not 
        present in input file B.
      - "report.txt" - a brief summary report (if --statout is used)
    
    Two junctions are considered equivalent if:
      - they come from different files
      - left and right positions of one junction are not more than "--distance"
        bases apart from the corresponding positions of another junction
      - the junction scores are equal or above the scoreThreshold
      - they are on the same strands

OPTIONS
  -h [ --help ] 
        Print this help message.

  --beta 
        This is a beta command. To run this command, you must pass the --beta 
        flag.

  -s [ --reference ] arg
        Reference file.

  -a [ --junctionsA ] arg
        input junction file A.

  -b [ --junctionsB ] arg
        input junction file B.

  -A [ --scoreThresholdA ] arg (=10)
        score threshold value for the input file A.

  -B [ --scoreThresholdB ] arg (=0)
        score threshold value for the input file B.

  -d [ --distance ] arg (=200)
        Max distance between coordinates of potentially compatible junctions.

  -l [ --minlength ] arg (=500)
        Minimum deletion junction length to be included into the difference 
        file.

  -o [ --output-prefix ] arg
        The path prefix for all the output reports.

  -S [ --statout ] 
        (Debug) Report various input file statistics. Experimental feature.


SUPPORTED FORMAT_VERSION
    1.5 or later