{ "info": { "author": "Joe Brown", "author_email": "brwnjm@gmail.com", "bugtrack_url": null, "classifiers": [ "Programming Language :: Python", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: Implementation :: PyPy" ], "description": "\n# covviz\n\nCoverage visualization; a many-sample coverage browser.\n\nThe aim of `covviz` is to highlight regions of significant\n(passing the user's z-score threshold) and sustained (beyond user specified\ndistance) deviation from the majority of samples. Significance is determined\nusing z-scores for all samples at all points using median absolute deviation.\nIn order for regions to be highlighted, points must be significant\nconsecutively throughout a user specified distance.\n\nIf you are analyzing a low number of samples, deviation may be irrelevant. In\nthis case, we can set `--min-samples` to be greater than our sample total\nto skip Z-threshold calculation and plot coverages for all samples at all\npoints.\n\n# The Python Package\n\n`covviz` is installable via `pip install -U covviz` and analyzes a bed3+\noutput format.\n\n## Usage\n\nTo analyze your coverage data it needs to be in bed3+ format and include a\nheader with sample IDs. The first three column headers are agnostic, but\nfor samples test_sample1, test_sample2, and test_sample3, this would look like:\n\n```\n#chrom start end sample1 sample2 sample3\n```\n\nThen CLI usage is:\n\n```\ncovviz $bed\n```\n\n### Custom Metadata (.ped)\n\nThere is support for non-indexcov .ped files, though you may have to change\nthe default column IDs pertaining to the column which contains the sample ID\nand the sex of the sample.\n\n```\ncovviz --ped $ped --sample-col sample_col --sex sex_col $bed\n```\n\n### Annotation Tracks\n\n![significant_regions](data/img/covviz_tracks.gif)\n\nCurrently we support GFF, VCF, and BED. GFF tracks are added using `--gff`\nwhere features are 'gene' and attributes have 'Name='. Feature type and\nattribute regex can be configured using `--gff-feature` and `--gff-attr`.\n\nVCF tracks (v4.1) are added with `--vcf` with the entire INFO string\nbeing displayed by default. Specifying `--vcf-info` with something like\n'CLNDN=' will grab just that field when using ClinVar variants. Including\nlarge INFO strings for all variants can dramatically increase the size\nof the covviz report.\n\nRegion based annotation tracks can be added using `--bed`. The name field\nwill be used to identify the regions when present.\n\nAnnotation tracks, `--gff`, `--vcf`, and `--bed`, may be specified\nmultiple times.\n\nIn all cases, 'chr' will be stripped from the chromosome names.\n\n# The Nextflow Workflow\n\nIf you're starting with alignment indexes, this workflow aims to simply the\nprocess of obtaining coverage and generating the coverage browser.\n\nWe use [indexcov](https://github.com/brentp/goleft/tree/master/indexcov)\nto quickly estimate the coverage across samples then find regions of large,\ncoverage-based anomalies.\n\nThe output of `indexcov` is then directly input into `covviz`.\n\n## Usage\n\nInstall `nextflow`:\n\n```\ncurl -s https://get.nextflow.io | bash\n```\n\nFull nextflow installation instructions are available at:\nhttps://www.nextflow.io/\n\nTo simplify prerequisite software installations and software version tracking,\nwe strongly recommend running `covviz` using Docker or Singularity. Docker\ninstallation instructions for your operating system are available at:\nhttps://docs.docker.com/install/\n\nThen, with Docker or Singularity we run:\n\n```\nnextflow run brwnj/covviz -latest -profile docker \\\n --indexes 'data/indexes/*.crai' \\\n --fai data/g1k_v37_decoy.fa.fai \\\n --gff data/Homo_sapiens.GRCh37.82.gff3.gz\n```\n\nWhich gives us `./results/covviz_report.html`.\n\n### Required arguments\n\n+ `--indexes`\n + quoted file path with wildcard ('*.crai') to cram or bam indexes\n+ `--fai`\n + file path to .fai reference index\n+ `--gff`\n + file path to gff matching genome build of `--indexes`\n\n### Workflow Options\n\n+ `--outdir`\n + output directory for results\n + default: \"./results\"\n+ `--sexchroms`\n + sex chromosomes as they are in `--indexes`\n + default: \"X,Y\"\n+ `--exclude`\n + regular expression of chromosomes to skip\n + default: \"^GL|^hs|^chrEBV$|M$|MT$|^NC|_random$|Un_|^HLA\\\\-|_alt$|hap\\\\d+$\"\n+ `--zthreshold`\n + a sample must greater than this many standard deviations in order to be found significant\n + default: 3.5\n+ `--distancethreshold`\n + consecutive significant points must span this distance in order to pass this filter\n + default: 150000\n+ `--slop`\n + leading and trailing segments added to significant regions to make them more visible\n + default: 500000\n+ `--ped`\n + custom metadata that will be merged with the .ped output of indexcov\n + default: false\n+ `--samplecol`\n + the column header for sample IDs in your custom ped file\n + default: \"sample_id\"\n\n\n# Report\n\n## Interactive example\n\nSee: https://brwnj.github.io/covviz/\n\n## Scaled chromosome coverage\n\nSignificant regions will be displayed in color atop a gray region which\nrepresents the upper and lower bounds of a given point minus any values\ndeemed significant.\n\n![significant_regions](data/img/significant_regions.png)\n\nWhen plotting fewer samples than `--min-samples`, the gray area plot\nwill not be displayed. Instead, all sample plot traces will be shown.\n\n![min_samples](data/img/min_samples.png)\n\n## Proportions covered\n\n![proportional_coverage](data/img/proportional_coverage.png)\n\nThe metadata table will be displayed below the plots.\n\n## Interaction\n\nClicking on plot traces highlights the line and searches the metadata.\nDouble-clicking de-selects lines, resets the plot, and de-selects\nsamples from the table. Clicking on the gene track launches a search\nfor the gene's respective Gene Card. In cases where genes overlap,\nmultiple windows/tabs will be opened.\n\n# License\n\ncovviz is free and unrestricted for non-commercial use. 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