gcpp(1)

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]

Arguments:

INPUT

The input BAM alignment file