GenomicConsensus (quiver, arrow)使用方法 | 序列 consensus

 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。

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./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~~