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