https://github.com/PacificBiosciences/GenomicConsensus
GenomicConsensus 是pacbio开发的，我个人非常不喜欢pacbio开发的工具，很难用。
安装这个GenomicConsensus也是废了我快半条老命。
这个工具的目的：Compute genomic consensus and call variants relative to the reference.
就是用一些reads来对最终的ref来进行纠错，这个模型适用性比较大，可以用在各个场合，尤其是我们在开发一些工具时，可以直接将这个嵌入到我们的工具中，减少开发量。
./bin/arrow -h
usage: variantCaller [-h] [--version] [--emit-tool-contract]
[--resolved-tool-contract RESOLVED_TOOL_CONTRACT]
[--log-file LOG_FILE]
[--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} | --debug | --quiet | -v]
--referenceFilename REFERENCEFILENAME -o OUTPUTFILENAMES
[-j NUMWORKERS] [--minConfidence MINCONFIDENCE]
[--minCoverage MINCOVERAGE]
[--noEvidenceConsensusCall {nocall,reference,lowercasereference}]
[--coverage COVERAGE] [--minMapQV MINMAPQV]
[--referenceWindow REFERENCEWINDOWSASSTRING]
[--alignmentSetRefWindows]
[--referenceWindowsFile REFERENCEWINDOWSASSTRING]
[--barcode _BARCODE] [--readStratum READSTRATUM]
[--minReadScore MINREADSCORE] [--minSnr MINHQREGIONSNR]
[--minZScore MINZSCORE] [--minAccuracy MINACCURACY]
[--algorithm {quiver,arrow,plurality,poa,best}]
[--parametersFile PARAMETERSFILE]
[--parametersSpec PARAMETERSSPEC]
[--maskRadius MASKRADIUS] [--maskErrorRate MASKERRORRATE]
[--pdb] [--notrace] [--pdbAtStartup] [--profile]
[--dumpEvidence [{variants,all,outliers}]]
[--evidenceDirectory EVIDENCEDIRECTORY] [--annotateGFF]
[--reportEffectiveCoverage] [--diploid]
[--queueSize QUEUESIZE] [--threaded]
[--referenceChunkSize REFERENCECHUNKSIZE]
[--fancyChunking] [--simpleChunking]
[--referenceChunkOverlap REFERENCECHUNKOVERLAP]
[--autoDisableHdf5ChunkCache AUTODISABLEHDF5CHUNKCACHE]
[--aligner {affine,simple}] [--refineDinucleotideRepeats]
[--noRefineDinucleotideRepeats] [--fast]
[--skipUnrecognizedContigs]
inputFilename
Compute genomic consensus and call variants relative to the reference.
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--emit-tool-contract Emit Tool Contract to stdout (default: False)
--resolved-tool-contract RESOLVED_TOOL_CONTRACT
Run Tool directly from a PacBio Resolved tool contract
(default: None)
--log-file LOG_FILE Write the log to file. Default(None) will write to
stdout. (default: None)
--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
Set log level (default: WARN)
--debug Alias for setting log level to DEBUG (default: False)
--quiet Alias for setting log level to CRITICAL to suppress
output. (default: False)
-v, --verbose Set the verbosity level. (default: None)
Basic required options:
inputFilename The input cmp.h5 or BAM alignment file
--referenceFilename REFERENCEFILENAME, --reference REFERENCEFILENAME, -r REFERENCEFILENAME
The filename of the reference FASTA file (default:
None)
-o OUTPUTFILENAMES, --outputFilename OUTPUTFILENAMES
The output filename(s), as a comma-separated
list.Valid output formats are .fa/.fasta, .fq/.fastq,
.gff, .vcf (default: [])
Parallelism:
-j NUMWORKERS, --numWorkers NUMWORKERS
The number of worker processes to be used (default: 1)
Output filtering:
--minConfidence MINCONFIDENCE, -q MINCONFIDENCE
The minimum confidence for a variant call to be output
to variants.{gff,vcf} (default: 40)
--minCoverage MINCOVERAGE, -x MINCOVERAGE
The minimum site coverage that must be achieved for
variant calls and consensus to be calculated for a
site. (default: 5)
--noEvidenceConsensusCall {nocall,reference,lowercasereference}
The consensus base that will be output for sites with
no effective coverage. (default: lowercasereference)
Read selection/filtering:
--coverage COVERAGE, -X COVERAGE
A designation of the maximum coverage level to be used
for analysis. Exact interpretation is algorithm-
specific. (default: 100)
--minMapQV MINMAPQV, -m MINMAPQV
The minimum MapQV for reads that will be used for
analysis. (default: 10)
--referenceWindow REFERENCEWINDOWSASSTRING, --referenceWindows REFERENCEWINDOWSASSTRING, -w REFERENCEWINDOWSASSTRING
The window (or multiple comma-delimited windows) of
the reference to be processed, in the format refGroup
:refStart-refEnd (default: entire reference).
(default: None)
--alignmentSetRefWindows
The window (or multiple comma-delimited windows) of
the reference to be processed, in the format refGroup
:refStart-refEnd will be pulled from the alignment
file. (default: False)
--referenceWindowsFile REFERENCEWINDOWSASSTRING, -W REFERENCEWINDOWSASSTRING
A file containing reference window designations, one
per line (default: None)
--barcode _BARCODE Only process reads with the given barcode name.
(default: None)
--readStratum READSTRATUM
A string of the form 'n/N', where n, and N are
integers, 0 <= n < N, designating that the reads are
to be deterministically split into N strata of roughly
even size, and stratum n is to be used for variant and
consensus calling. This is mostly useful for Quiver
development. (default: None)
--minReadScore MINREADSCORE
The minimum ReadScore for reads that will be used for
analysis (arrow-only). (default: 0.65)
--minSnr MINHQREGIONSNR
The minimum acceptable signal-to-noise over all
channels for reads that will be used for analysis
(arrow-only). (default: 3.75)
--minZScore MINZSCORE
The minimum acceptable z-score for reads that will be
used for analysis (arrow-only). (default: -3.5)
--minAccuracy MINACCURACY
The minimum acceptable window-global alignment
accuracy for reads that will be used for the analysis
(arrow-only). (default: 0.82)
Algorithm and parameter settings:
--algorithm {quiver,arrow,plurality,poa,best}
--parametersFile PARAMETERSFILE, -P PARAMETERSFILE
Parameter set filename (such as ArrowParameters.json
or QuiverParameters.ini), or directory D such that
either D/*/GenomicConsensus/QuiverParameters.ini, or
D/GenomicConsensus/QuiverParameters.ini, is found. In
the former case, the lexically largest path is chosen.
(default: None)
--parametersSpec PARAMETERSSPEC, -p PARAMETERSSPEC
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 (default: auto)
--maskRadius MASKRADIUS
Radius of window to use when excluding local regions
for exceeding maskMinErrorRate, where 0 disables any
filtering (arrow-only). (default: 3)
--maskErrorRate MASKERRORRATE
Maximum local error rate before the local region
defined by maskRadius is excluded from polishing
(arrow-only). (default: 0.7)
Verbosity and debugging/profiling:
--pdb Enable Python debugger (default: False)
--notrace Suppress stacktrace for exceptions (to simplify
testing) (default: False)
--pdbAtStartup Drop into Python debugger at startup (requires ipdb)
(default: False)
--profile Enable Python-level profiling (using cProfile).
(default: False)
--dumpEvidence [{variants,all,outliers}], -d [{variants,all,outliers}]
--evidenceDirectory EVIDENCEDIRECTORY
--annotateGFF Augment GFF variant records with additional
information (default: False)
--reportEffectiveCoverage
Additionally record the *post-filtering* coverage at
variant sites (default: False)
Advanced configuration options:
--diploid Enable detection of heterozygous variants
(experimental) (default: False)
--queueSize QUEUESIZE, -Q QUEUESIZE
--threaded, -T Run threads instead of processes (for debugging
purposes only) (default: False)
--referenceChunkSize REFERENCECHUNKSIZE, -C REFERENCECHUNKSIZE
--fancyChunking Adaptive reference chunking designed to handle
coverage cutouts better (default: True)
--simpleChunking Disable adaptive reference chunking (default: True)
--referenceChunkOverlap REFERENCECHUNKOVERLAP
--autoDisableHdf5ChunkCache AUTODISABLEHDF5CHUNKCACHE
Disable the HDF5 chunk cache when the number of
datasets in the cmp.h5 exceeds the given threshold
(default: 500)
--aligner {affine,simple}, -a {affine,simple}
The pairwise alignment algorithm that will be used to
produce variant calls from the consensus (Quiver
only). (default: affine)
--refineDinucleotideRepeats
Require quiver maximum likelihood search to try one
less/more repeat copy in dinucleotide repeats, which
seem to be the most frequent cause of suboptimal
convergence (getting trapped in local optimum) (Quiver
only) (default: True)
--noRefineDinucleotideRepeats
Disable dinucleotide refinement (default: True)
--fast Cut some corners to run faster. Unsupported! (default:
False)
--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. (default: False)
待续~~