igv-reports

Below are examples of using IGV-Reports to create variant reports. The examples cover a variety of input file formats and options. For more information on command line arguments see the IGV Reports documentation.

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.

Create a variant report from a VCF file with title, header, and footer. (Example output)

create_reports test/data/variants/variants.vcf.gz
–genome hg38
–flanking 1000
–info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC
–sample-columns DP GQ
–tracks test/data/variants/variants.vcf.gz test/data/variants/recalibrated.bam
–title “IGV Variant Inspector”
–header test/example_header.html
–footer test/example_footer.html
–output example_vcf.html

Create a variant report from a VCF file with genotypes and sample information. (Example output)

create_reports test/data/variants/1kg_genotypes.vcf
–genome hg19
–sampleinfo test/data/variants/1kg_sampleinfo.txt
–tracks test/data/variants/1kg_genotypes.vcf
–output example_sampleinfo.html

Create a variant report from a BED file. (Example output)

create_reports test/data/variants/variants.bed
–genome hg38
–flanking 1000
–tracks test/data/variants/variants.bed test/data/variants/recalibrated.bam
–output example_bed.html

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

create_reports 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)

create_reports 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)

create_reports test/data/variants/SKBR3_Sniffles_tra.vcf
–genome hg19
–flanking 1000
–maxlen 10500
–info-columns SVLEN
–tracks test/data/variants/SKBR3_Sniffles_sv.vcf test/data/variants/SKBR3_translocations.ill.bam
–output example_sv.html

Create a structural variant report from a bedpe file with two locations (BEDPE format). (Example output)

create_reports test/data/variants/SKBR3_Sniffles_tra.bedpe
–genome hg19
–flanking 1000
–tracks test/data/variants/SKBR3_Sniffles_variants_tra.vcf test/data/variants/SKBR3_translocations.ill.bam
–output example_bedpe.html

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

create_reports test/data/variants/variants.vcf.gz
–twobit –twobit https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit
–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)

create_reports 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

create_reports 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. Example output

create_reports 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_fusions.html

Create a report containing wig and bedgraph files. Example output

create_reports 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

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

create_reports 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

Create a variant report from a VCF file with Tabulator Template. (Example output)

create_reports test/data/variants/variants.vcf.gz
–genome hg38
–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
–tabulator
–filter-config test/data/variants/filter_config.yaml
–output example_vcf_tabulator.html

Example use of samtools --exclude-flags option

Use --exclude-flags value of 512 to include duplicate alignments in report by specifying a samtools --exclude-flags value. Default value is 1536 which filters duplicates and vendor-failed reads.

create_reports test/data/dups/dups.bed
–genome hg19
–exclude-flags 512
–tracks test/data/dups/dups.bam
–output example_dups.html

Example use of -no-embed option to use external URL references for tracks in the report.

In this example the --no-embed option is used to prevent embedding of the data in the report. Instead the data files are referenced as URLs. This is an unusual usage pattern for IGV Reports, but may be useful in some situations. Note that when using --no-embed local files are not supported, only URLs.

create_reports test/data/variants/variants.vcf.gz
–genome hg38
–no-embed
–tracks https://raw.githubusercontent.com/igvteam/igv-reports/refs/heads/master/test/data/variants/variants.vcf.gz https://raw.githubusercontent.com/igvteam/igv-reports/refs/heads/master/test/data/variants/recalibrated.bam
–output example_noembed.html

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