NAME

       gcpp  -  Compute  genomic  consensus  from  alignments  and  call variants relative to the
       reference

SYNOPSIS

       gcpp [options] INPUT

DESCRIPTION

       Compute genomic consensus from alignments and call variants relative to the reference.

   Basic required options:
       --referenceFilename,--reference,-r
              The filename of the reference FASTA file.

       --outputFilenames,-o
              The output filename(s),  as  a  comma-separated  list.  Valid  output  formats  are
              .fa/.fasta, .fq/.fastq, .gff, .vcf

   Parallelism:
       --numThreads,-j
              The number of threads to be used.  [1]

   Output filtering:
       --minConfidence,-q
              The minimum confidence for a variant call to be output to variants.{gff,vcf} [40]

       --minCoverage,-x
              The  minimum site coverage that must be achieved for variant calls and consensus to
              be calculated for a site. [5]

       --noEvidenceConsensusCall
              The consensus base that will be  output  for  sites  with  no  effective  coverage.
              ["lowercasereference"]

   Read selection/filtering:
       --coverage,-X
              A  designation  of  the  maximum  coverage  level  to  be  used for analysis. Exact
              interpretation is algorithm-specific. [100]

       --minAccuracy
              The minimum acceptable window-global alignment accuracy for reads that will be used
              for the analysis (arrow-only). [0.82]

       --minMapQV,-m
              The minimum MapQV for reads that will be used for analysis. [10]

       --minReadScore
              The minimum ReadScore for reads that will be used for analysis (arrow-only). [0.65]

       --minSnr
              The  minimum  acceptable  signal-to-noise  over all channels for reads that will be
              used for analysis (arrow-only). [3.75]

       --minZScore
              The  minimum  acceptable  z-score  for  reads  that  will  be  used  for   analysis
              (arrow-only). [-3.4]

       --barcode,--barcodes
              Comma-separated  list  of  barcode  pairs  to  analyze,  either  by  name,  such as
              'lbc1--lbc1', or by index,  such  as  '0--0'.  NOTE:  Filtering  barcodes  by  name
              requires a barcode file.

       --barcodeFile
              Fasta file of the barcode sequences used. NOTE: Only used to find barcode names

       --referenceWindow,--referenceWindows,-w
              The  window (or multiple comma-delimited windows) of the reference to be processed,
              in the format refGroup:refStart-refEnd (default: entire reference).

       --referenceWindowsFile,-W
              A file containing reference window designations, one per line

   Algorithm and parameter settings:
       --algorithm
              The consensus algorithm used.  ["arrow"]

       --maskRadius
              Radius  of  window  to   use   when   excluding   local   regions   for   exceeding
              maskMinErrorRate, where 0 disables any filtering (arrow-only). [0]

       --maskErrorRate
              Maximum  local  error rate before the local region defined bymaskRadius is excluded
              from polishing (arrow-only).  [0]

       --parametersFile,-P
              Parameter set filename (such as ArrowParameters.json or  QuiverParameters.ini),  or
              directory   D  such  that  either  D/*/GenomicConsensus/QuiverParameters  .ini,  or
              D/GenomicConsensus/QuiverParameters.i ni,  is  found.   In  the  former  case,  the
              lexically largest path is chosen.

       --parametersSpec,-p
              Name of parameter set (chemistry.model) to select from the parameters file, or just
              the name of the chemistry, in which  case  the  best  available  model  is  chosen.
              Default  is  'auto',  which  selects the best parameter set from the alignment data
              ["auto"]

       --maxIterations
              Maximum number of iterations to polish the template. [40]

       --maxPoaCoverage
              Maximum number of sequences to use for consensus calling. [11]

       --mutationSeparation
              Find the best mutations within a separation window for iterative polishing. [10]

       --mutationNeighborhood
              Find nearby mutations within neighborhood for iterative polishing.  [10]

       --readStumpinessThreshold
              Filter out reads whose aligned length along a subread is lower than a percentage of
              its corresponding reference length. [0.1]

   Verbosity and debugging:
       --logFile
              Log to a file, instead of STDERR.

       --dumpEvidence,-d
              Dump evidence data

       --evidenceDirectory
              Directory to dump evidence into.

       --annotateGFF
              Augment GFF variant records with additional information

       --reportEffectiveCoverage
              Additionally record the *post-filtering* coverage at variant sites

   Advanced configuration options:
       --referenceChunkSize,-C
              Size of reference chunks. [500]

       --referenceChunkOverlap
              Size of reference chunk overlaps.  [5]

       --simpleChunking
              Disable adaptive reference chunking.

       --diploid
              Enable detection of heterozygous variants (experimental)

       --fast Cut some corners to run faster.  Unsupported!

       --skipUnrecognizedContigs
              Do  not abort when told to process a reference window (via -w/--referenceWindow[s])
              that has no aligned coverage.  Outputs emptyish files if  there  are  no  remaining
              non-degenerate windows.  Only intended for use by smrtpipe scatter/gather.

       --sortStrategy
              Read sortiing strategy ["longest_and_strand_balanced"]

       --minPoaCoverage
              Minimum  number  of  reads  required within a window to call consensus and variants
              using arrow or poa. [3]

OPTIONS

       -h,--help
              Output this help.

       --log-level,--logLevel
              Set log level. ["INFO"]

       --version
              Output version info.

       --emit-tool-contract
              Emit tool contract.

       --resolved-tool-contract
              Use args from resolved tool contract.

   Arguments:
       INPUT  The input BAM alignment file

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.