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Creates self-contained html pages for visual variant review with IGV (igv.js).

Project description

igv-reports

A Python application to generate self-contained HTML reports that consist of a table of genomic sites or regions and associated IGV views for each site. The generated HTML page contains all data neccessary for IGV as uuencoded blobs. It can be opened within a web browser as a static page, with no depenency on the original input files.

NEW - alignments marked "duplicate" are now filtered by default. See the --exclude-flags option.

Installation

Prerequisites

igv-reports requires Python 3.6 or greater.

As with all Python projects, use of a virtual environment is recommended. Instructions for creating a virtual environment using conda follow.

1. Install Anaconda from https://docs.anaconda.com/anaconda/

2. Create a virtual environment

conda create -n igvreports python=3.7.1
conda activate igvreports

Installing igv-reports

pip install igv-reports

igv-reports requires the package pysam version 0.19.1 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;
"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."

conda config --add channels r
conda config --add channels bioconda
conda install pysam

Creating a report

A report consists of a table of sites or regions and an associated IGV view for each site. 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.
  • 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 for generic tab delimited sites file

    • --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

    • --genome New An igv.js genome identifier (e.g. hg38). If supplied fasta, ideogram, and the default annotation track for the specified genome will be used.
    • --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 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.
    • --ideogram FILE. Ideogram file in UCSC cytoIdeo format.
    • --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 for more details.
    • --idlink URL tempate for information link for VCF ID values. The token $$ will be substituted with the ID value. Example: --idlink 'https://www.ncbi.nlm.nih.gov/snp/?term=$$'

Track file formats:

Currently supported track file formats are BAM, CRAM, VCF, BED, GFF3, and GTF. 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. The repository can be downloaded as a zip archive here 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 and can be viewed here.

NEW (version 1.5.0) - Create a report using a genome identifier: (Example output)

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 examples/example_genome.html

Create a variant report from a VCF file: (Example output)

create_report test/data/variants/variants.vcf.gz \
http://s3.amazonaws.com/igv.broadinstitute.org/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 examples/example_vcf.html

Create a variant report with tracks defined in an igv.js track config json file: (Example output)

create_report test/data/variants/variants.vcf.gz \
https://s3.amazonaws.com/igv.broadinstitute.org/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 examples/example_config.html

Create a variant report from a TCGA MAF file: (Example output)

create_report test/data/variants/tcga_test.maf \
https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta \
--ideogram test/data/hg19/cytoBandIdeo.txt \
--flanking 1000 \
--info-columns Chromosome Start_position End_position Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS \
--tracks  https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz \
--output examples/example_maf.html

Create a variant report from a generic tab-delimited file: (Example output)

create_report test/data/variants/test.maflite.tsv \
https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta \
--sequence 1 --begin 2 --end 3 \
--ideogram test/data/hg19/cytoBandIdeo.txt \
--flanking 1000 \
--info-columns chr start end ref_allele alt_allele \
--tracks https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz \
--output examples/example_tab.html

NEW (version 1.5.0) - Create a structural variant report from a bedpe file with two locations (BEDPE format): (Example output)

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 https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz \
--output examples/example_bedpe.html

Create a variant report with custom ID link urls: (Example output)

create_report test/data/variants/1kg_phase3_sites.vcf.gz \
https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta \
--ideogram test/data/hg19/cytoBandIdeo.txt \
--flanking 1000 \
--tracks test/data/variants/1kg_phase3_sites.vcf.gz test/data/variants/NA12878_lowcoverage.bam https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz \
--idlink 'https://www.ncbi.nlm.nih.gov/snp/?term=$$' \
--output examples/example_idlink.html

Create a junction report from a splice-junction bed file: (Example output)

create_report test/data/junctions/Introns.38.bed \
https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa \
--type junction \
--ideogram test/data/hg38/cytoBandIdeo.txt \
--track-config test/data/junctions/tracks.json \
--info-columns TCGA GTEx variant_name \
--title "Sample A" \
--output examples/example_junctions.html

Use of info-columns-prefixes option. Variant track only, no alignments. (Example output)

create_report test/data/infofields/consensus.filtered.ann.vcf \
--genome hg19 \
--flanking 1000 \
--info-columns cosmic_gene \
--info-columns-prefixes clinvar \
--tracks test/data/infofields/consensus.filtered.ann.vcf \
--output https://igv.org/igv-reports/examples/1.5.1/example_ann.html 

Use --exclude-flags option to include duplicate alignments in report. Default value is 1536 which filters duplicates and vendor-failed reads.

create_report test/data/dups/dups.bed \
--genome hg19 \
--exclude-flags 512 \
--tracks test/data/dups/dups.bam \
--output examples/example_dups.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.

create_datauri test/data/variants/variants.vcf.gz

Convert a slice of a local bam file to a datauri.

create_datauri --region chr5:474,969-475,009 test/data/variants/recalibrated.bam 

Convert a remote bam file to a datauri.

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

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