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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 of coverage depth 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# Getting started\n\n## From alignments (.bam and/or .cram)\n\nAlignments must be indexed. The input for the `covviz` workflow are the indexes\nof the alignments. For BAM, that would be .bai, and .crai for CRAM. Indexes\ncan be generated using [samtools](https://github.com/samtools/samtools) on your\nsorted alignments:\n\n```\nsamtools index mybam.bam\n# generates mybam.bam.bai\n```\n\n### Installation and usage\n\nInstall [Nextflow](https://www.nextflow.io/) if you don't already have it. The only\ndependency is Java 8 or later, then you run:\n\n```\ncurl -s https://get.nextflow.io | bash\n```\n\nOr via [Bioconda](https://bioconda.github.io/recipes/nextflow/README.html) using:\n\n```\nconda install -c bioconda nextflow\n```\n\nFull nextflow installation instructions are available at:\nhttps://www.nextflow.io/\n\nThere is no need to download the covviz code prior to execution or any software dependencies\nwhen using a container service like Docker or Singularity.\n\n### Docker/Singularity\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\nA complete list of arguments can be displayed using:\n\n```\nnextflow run brwnj/covviz -latest --help\n```\n\n### Nextflow arguments\n\nIn the example above `-latest` pulls whatever the latest `covviz` code exists on GitHub\nprior to execution and `-profile docker` sets `-with-docker` within Nextflow.\n\nOther notable options are `-resume`, which when running a workflow a second will start\nwhere previous runs of the workflow left off; and `-work-dir` which sets the location of\nall intermediate files generated throughout the workflow.\n\n## From coverage intervals (.bed)\n\nThe `covviz` CLI accepts bed3+ as input. If you've already generated your coverage\nfiles you can start here and not the Nextflow workflow.\n\nIf you would prefer to run `indexcov` yourself across your .bai or .crai files,\nthe workflow above simply runs:\n\n```\nfai=data/g1k_v37_decoy.fa.fai\ngoleft indexcov --directory myproject --fai $fai *.crai\n```\n\nThis will generate the expected inputs in their anticipated formats for the `covviz` CLI.\n\n### Expected file format\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\n### Installation of CLI and usage\n\nTo install the `covviz` Python package use:\n\n```\npip install -U covviz\n```\n\nThen CLI usage is:\n\n```\ncovviz $bed\n```\n\nA complete list of arguments can be displayed using:\n\n```\ncovviz --help\n```\n\n### Adding 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### Adding 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# Interpreting the output\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","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrwnj%2Fcovviz","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrwnj%2Fcovviz","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrwnj%2Fcovviz/lists"}