NAME¶

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

SYNOPSIS¶

gcpp [options] INPUT

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

--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

--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"]

--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: 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]

--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

--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]

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

October 2018

gcpp 3.1.0