Metadata-Version: 2.1
Name: igv-reports
Version: 1.14.0
Summary: Creates self-contained html pages for visual variant review with IGV (igv.js).
Home-page: https://github.com/igvteam/igv-reports
Author: Jim Robinson
License: MIT
Description: # igv-reports
        
        igv-reports - A Python application to generate self-contained HTML reports for variant review and other genomic
        applications. Reports consist of a table of genomic sites and an embedded IGV genome browser for viewing data for each
        site. The tool extracts slices of data for each site and embeds the data as blobs in the HTML report file. The report
        can be opened in a web browser as a static page, with no depenency on the original input files.
        
        ## Installation
        
        #### Prerequisites
        
        igv-reports __requires Python 3.8__ or greater.
        
        #### Installing igv-reports
        
        ```bash
        pip install igv-reports
        ```
        
        igv-reports requires the package _pysam_ version 0.22.0 or greater, which should be installed automatically. However, on
        OSX this sometimes fails due to missing dependent libraries. This can be fixed following the procedure below, from the
        pysam [docs](https://pysam.readthedocs.io/en/latest/installation.html#installation);  
        _"The recommended way to install pysam is through conda/bioconda.
        This will install pysam from the bioconda channel and automatically makes sure that dependencies are installed.
        Also, compilation flags will be set automatically, which will potentially save a lot of trouble on OS X."_
        
        ```bash
        conda config --add channels r
        conda config --add channels bioconda
        conda install pysam
        ```
        
        ## Creating a report
        
        Reports are created with the command line script ```create_report```, or
        alternatively ```python igv_reports/report.py```. Command line arguments
        are described below. Although _--tracks_ is optional, a typical report will include at least an alignment track
        (BAM or CRAM) file from which the variants were called.
        
        **Arguments:**
        
        * Required
            * __sites__   VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites. Tabix indexed files are
              supported and strongly recommended for large files.
            * __--fasta__   Reference fasta file; must be indexed. This argument should be ommited if --genome is used,
              otherwise it is required.
            * __--genome__  An igv.js genome identifier (e.g. hg38). If supplied fasta, ideogram, and the default annotation
              track for the specified genome will be used.*
        
        * The arguments _begin_, _end_, and _sequence_ are required for a generic tab delimited __sites__ file.
            * __--begin__ INT. Column of start chromosomal position for __sites__ file. Used for generic tab delimited input.
            * __--end__ INT. Column of end chromosomal position for __sites__. Used for generic tab delimited input.
            * __--sequence__ INT. Column of sequence (chromosome) name.
        
        * Optional coordinate system flag for generic tab delimited __sites__ file only
            * __--zero_based__  Specify that the position in the __sites__ file is 0-based (e.g. UCSC files) rather than
              1-based. Default is ```false```.
        
        * Optional
            * __--ideogram__ FILE. Ideogram file in UCSC cytoIdeo format. Useful when __fasta__ is used to specify the
              reference.
            * __--tracks__ LIST. Space-delimited list of track files, see below for supported formats. If both *tracks* and
              *track-config* are specified *tracks* will appear first by default.
            * __--track-config__  FILE. File containing array of json configuration objects for igv.js tracks. See
              the [igv.js wiki](https://github.com/igvteam/igv.js/wiki/Tracks-2.0) for more details. This option allows
              customization of track parameters. When using this option, the track ```url``` and ```indexURL``` properties
              should be set to the paths of the respective files.
            * __--roi__ LIST. Space-delimited list of region-of-interest (ROI) files.
              See [igv.js wiki](https://github.com/igvteam/igv.js/wiki/Regions-of-Interest).
            * __--template__ FILE. HTML template file.
            * __--output__ FILE. Output file name; default="igvjs_viewer.html".
            * __--info-columns__ LIST. Space delimited list of info field names to include in the variant table. If __sites__ is
              a VCF file these are the info ID values. If __sites__ is a tab delimited format these are column names.
            * __--info-columns-prefixes__ LIST. For VCF based reports only. Space delimited list of prefixes of VCF info field
              IDs to include in the variant table. Any info field with ID starting with one of the listed values will be
              included.
            * __--samples__ LIST. Space delimited list of sample (i.e. genotypes) names. Used in conjunction with _
              _--sample-columns__.
            * __--sample-columns__ LIST. Space delimited list of VCF sample FORMAT field names to include in the variant table.
              If __--samples__ is specified columns will be restricted to those samples, otherwise all samples will be included.
            * __--flanking__ INT. Genomic region to include either side of variant; default=1000.
            * __--standalone__ Embed all JavaScript referenced via ```<script>``` tags in the page.
            * __--sort__ Applies to alignment tracks only. If specified alignments are initally sorted by the specified option.
              Supported values include  ```BASE, STRAND, INSERT_SIZE, MATE_CHR, and NONE```. Default value is ```BASE``` for
              single nucleotide variants, ```NONE``` (no sorting) otherwise. See the igv.js documentation for more information.
            * __--exclude-flags__  INT. Value is passed to samtools as "-F" flag. Used to filter alignments. Default value is
              1536 which filters alignments marked "duplicate" or "vendor failed". To include all alignments
              use ```--exclude-flags 0```. See [samtools documentation](http://www.htslib.org/doc/samtools-view.html) for more
              details.
            * __--idlink__ URL tempate for information link for VCF ID values. The token $$ will be substituted with the ID
              value. Example: ```--idlink 'https://www.ncbi.nlm.nih.gov/snp/?term=$$'```
            * __--no-embed__ Don't embed data. Fasta and track URLs are referenced unchanged. The resulting report is dependent
              on the original data files, which must be specified as URLs. Local files are not supported with this option.
            * __--subsample__ FLOAT. Output only a portion of input alignments (0.0 -> 1.0). See `samtools view` documentation
              for more details
            * __--maxlen__ INT. Maximum length of a variant (SV) to show in a single view. Variants exceeding this length will
              be shown in a split-screen (multilocus) view. default = 10000
            * __--translate-sequence-track__ Three-frame Translate sequence track
        
        **Track file formats:**
        
        Currently supported track file formats are BAM, CRAM, VCF, BED, GFF3, GTF, WIG, and BEDGRAPH. FASTA. BAM, CRAM, and
        VCF  
        files must be indexed. Tabix is supported and it is recommended that all large files be indexed.
        
        ## Examples
        
        Data for the examples are available in the github
        repository [https://github.com/igvteam/igv-reports](https://github.com/igvteam/igv-reports). The repository can be
        downloaded as a zip archive
        here [https://github.com/igvteam/igv-reports/archive/refs/heads/master.zip](https://github.com/igvteam/igv-reports/archive/refs/heads/master.zip).
        It is assumed that the examples are run from the root directory of the repository. Output html is written to the
        examples directory.
        
        #### Create a variant report from a VCF file: ([Example output](https://igvteam.github.io/igv-reports/examples/example_vcf.html))
        
        ```bash
        
        create_report test/data/variants/variants.vcf.gz \
        --fasta https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa \
        --ideogram test/data/hg38/cytoBandIdeo.txt \
        --flanking 1000 \
        --info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
        --samples reads_1_fastq \
        --sample-columns DP GQ \
        --tracks test/data/variants/variants.vcf.gz test/data/variants/recalibrated.bam test/data/hg38/refGene.txt.gz \
        --output example_vcf.html
        
        ```
        
        #### Create a variant report from a BED  file: ([Example output](https://igvteam.github.io/igv-reports/examples/example_bed.html))
        
        ```bash
        echo bed
        create_report test/data/variants/variants.bed \
        --genome hg38 \
        --flanking 1000 \
        --info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
        --tracks test/data/variants/variants.bed test/data/variants/recalibrated.bam \
        --output example_genome.html
        ```
        
        #### Create a variant report from a TCGA MAF file: ([Example output](https://igvteam.github.io/igv-reports/examples/example_maf.html))
        
        ```bash
        
        create_report test/data/variants/tcga_test.maf \
        --genome hg19 \
        --flanking 1000 \
        --info-columns Chromosome Start_position End_position Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS \
        --tracks test/data/variants/tcga_test.maf \
        --output example_maf.html
        
        ```
        
        #### Create a variant report from a generic tab-delimited file: ([Example output](https://igvteam.github.io/igv-reports/examples/example_tab.html))
        
        ```bash
        
        create_report test/data/variants/test.maflite.tsv \
        --genome hg19 \
        --sequence 1 --begin 2 --end 3 \
        --flanking 1000 \
        --info-columns chr start end ref_allele alt_allele \
        --output example_tab.html
        
        ```
        
        #### Create a structural variant report from a vcf file with CHR2 and END info fields: ([Example output](https://igvteam.github.io/igv-reports/examples/example_sv.html))
        
        ```bash
        create_report test/data/variants/SKBR3_Sniffles_sv.vcf \
        --genome hg19 \
        --flanking 1000 \
        --maxlen 10500 \
        --info-columns SVLEN \
        --tracks test/data/variants/SKBR3_Sniffles_sv.vcf https://igv-genepattern-org.s3.amazonaws.com/test/bam/reads_lr_skbr3.sampled.bam \
        --output example_sv.html 
        
        ```
        
        #### Create a structural variant report from a bedpe file with two locations (BEDPE format): ([Example output](https://igvteam.github.io/igv-reports/examples/example_bedpe.html))
        
        ```bash
        
        create_report test/data/variants/SKBR3_Sniffles_tra.bedpe \
        --genome hg19 \
        --flanking 1000 \
        --tracks test/data/variants/SKBR3_Sniffles_variants_tra.vcf test/data/variants/SKBR3.ill.bam \
        --output example_bedpe.html
        ```
        
        #### Create a report using a genome identifier: ([Example output](https://igvteam.github.io/igv-reports/examples/example_genome.html)\)
        
        ```bash
        create_report test/data/variants/variants.vcf.gz \
        --genome hg38 \
        --flanking 1000 \
        --info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
        --tracks test/data/variants/variants.vcf.gz test/data/variants/recalibrated.bam \
        --output example_genome.html
        ```
        
        #### Create a variant report with tracks defined in an [igv.js track config json file](https://github.com/igvteam/igv-reports/tree/master/test/data/variants/trackConfigs.json): ([Example output](https://igvteam.github.io/igv-reports/examples/example_config.html))
        
        ``` bash
        create_report test/data/variants/variants.vcf.gz \
        --fasta https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa \
        --ideogram test/data/hg38/cytoBandIdeo.txt \
        --flanking 1000 \
        --info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
        --track-config test/data/variants/trackConfigs.json \
        --output example_config.html
        ```
        
        #### Create a variant report with custom ID link urls: ([Example output](https://igvteam.github.io/igv-reports/examples/example_idlink.html))
        
        ```bash
        
        create_report test/data/variants/1kg_phase3_sites.vcf.gz \
        --genome hg19 \
        --flanking 1000 \
        --tracks test/data/variants/1kg_phase3_sites.vcf.gz test/data/variants/NA12878_lowcoverage.bam \
        --idlink 'https://www.ncbi.nlm.nih.gov/snp/?term=$$' \
        --output example_idlink.html
        
        ```
        
        #### Create a junction report from a splice-junction bed file: ([Example output](https://igvteam.github.io/igv-reports/examples/example_junctions.html))
        
        ```bash
        create_report test/data/junctions/Introns.38.bed \
        --genome hg38 \
        --type junction \
        --track-config test/data/junctions/tracks.json \
        --info-columns TCGA GTEx variant_name \
        --title "Sample A" \
        --output example_junctions.html
        ```
        
        #### Create a fusion report from a Trinity fusion json file:
        
        ```bash
        create_report test/data/fusion/igv.fusion_inspector_web.json \
        --fasta test/data/fusion/igv.genome.fa  \
        --template igv_reports/templates/fusion_template.html  \  
        --track-config test/data/fusion/tracks.json  \
        --output example_fusion.html
        ```
        
        #### Create a report containing wig and bedgraph files
        
        ```bash
        create_report test/data/wig/regions.bed \
        --genome hg19 \
        --exclude-flags 512 \
        --tracks test/data/wig/ucsc.bedgraph test/data/wig/mixed_step.wig test/data/wig/variable_step.wig \
        --output example_wig.html
        
        ```
        
        #### Use of ```info-columns-prefixes``` option. Variant track only, no alignments. ([Example output](https://igvteam.github.io/igv-reports/examples/example_ann.html))
        
        ```bash
        python igv_reports/report.py test/data/annotated_vcf/consensus.filtered.ann.vcf \
        --genome hg19 \
        --flanking 1000 \
        --info-columns cosmic_gene \
        --info-columns-prefixes clinvar \
        --tracks test/data/annotated_vcf/consensus.filtered.ann.vcf \
        --output example_ann.html 
        ```
        
        #### Use ```--exclude-flags``` option to include duplicate alignments in report by specifying a samtools `--exclude-flags` value. Default value is 1536 which filters duplicates and vendor-failed reads.
        
        ```bash
        create_report test/data/dups/dups.bed \
        --genome hg19 \
        --exclude-flags 512 \
        --tracks test/data/dups/dups.bam \
        --output example_dups.html
        ```
        
        ### Use ```-no-embed``` option to use external URL references for tracks in the report.
        
        ```bash
        create_report test/data/variants/variants.vcf.gz \
        --genome hg38 \
        --no-embed \
        --tracks https://igv-genepattern-org.s3.amazonaws.com/test/reports/variants.vcf.gz https://igv-genepattern-org.s3.amazonaws.com/test/reports/recalibrated.bam \
        --output example_noembed.html
        
        ```
        
        #### Converting genomic files to data URIs for use in igv.js
        
        The script ```create_datauri``` (```python igv_reports/datauri.py```) converts the contents of a file to a data uri for
        use in igv.js. The datauri will be printed to stdout.  *NOTE* It is not neccessary to run this script explicitly to
        create a report, it is documented here
        for use with stand-alone igv.js.
        
        **Convert a gzipped vcf file to a datauri.**
        
        ```bash
        create_datauri test/data/variants/variants.vcf.gz
        
        ```
        
        **Convert a slice of a local bam file to a datauri.**
        
        ```bash
        create_datauri --region chr5:474,969-475,009 test/data/variants/recalibrated.bam 
        ```
        
        **Convert a remote bam file to a datauri.**
        
        ```bash
        create_datauri --region chr5:474,969-475,009 https://1000genomes.s3.amazonaws.com/phase3/data/NA12878/alignment/NA12878.mapped.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
        ```
        
        ## [_Release Notes_](https://github.com/igvteam/igv-reports/releases)
        
Keywords: igv,bioinformatics,genomics,visualization,variant
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Development Status :: 4 - Beta 
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics 
Description-Content-Type: text/markdown
