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### Create a variant report from a VCF file with title, header, and footer. ([Example output](examples/example_vcf.html))
python igv_reports/report.py 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](examples/example_sampleinfo.html))
python igv_reports/report.py 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](examples/example_bed.html))
python igv_reports/report.py 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](examples/example_maf.html))
python igv_reports/report.py 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](examples/example_tab.html))
python igv_reports/report.py 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](examples/example_sv.html))
python igv_reports/report.py 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](examples/example_bedpe.html))
python igv_reports/report.py 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](https://github.com/igvteam/igv-reports/tree/master/test/data/variants/trackConfigs.json). ([Example output](examples/example_config.html))
python igv_reports/report.py 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](examples/example_idlink.html))
python igv_reports/report.py 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](examples/example_junctions.html)
python igv_reports/report.py 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](examples/example_fusions.html)
python igv_reports/report.py 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](examples/example_wig.html)
python igv_reports/report.py 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](examples/example_ann.html))
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
#### Create a variant report from a VCF file with Tabulator Template. ([Example output](examples/example_vcf_tabulator.html))
python igv_reports/report.py 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
python igv_reports/report.py 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.
python igv_reports/report.py 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