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update examples
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jrobinso committed Dec 23, 2023
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Expand Up @@ -111,7 +111,7 @@ here [https://github.com/igvteam/igv-reports/archive/refs/heads/master.zip](http
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://igv.org/igv-reports/examples/1.9.0/example_vcf.html))
#### Create a variant report from a VCF file: ([Example output](https://igvteam.github.io/igv-reports/examples/example_vcf.html))

```bash

Expand All @@ -127,7 +127,7 @@ create_report test/data/variants/variants.vcf.gz \

```

#### Create a variant report from a BED file: ([Example output](https://igv.org/igv-reports/examples/1.9.0/example_bed.html))
#### Create a variant report from a BED file: ([Example output](https://igvteam.github.io/igv-reports/examples/example_bed.html))

```bash
echo bed
Expand All @@ -139,7 +139,7 @@ create_report test/data/variants/variants.bed \
--output example_genome.html
```

#### Create a variant report from a TCGA MAF file: ([Example output](https://igv.org/igv-reports/examples/1.9.0/example_maf.html))
#### Create a variant report from a TCGA MAF file: ([Example output](https://igvteam.github.io/igv-reports/examples/example_maf.html))

```bash

Expand All @@ -152,7 +152,7 @@ create_report test/data/variants/tcga_test.maf \

```

#### Create a variant report from a generic tab-delimited file: ([Example output](https://igv.org/igv-reports/examples/1.9.0/example_tab.html))
#### Create a variant report from a generic tab-delimited file: ([Example output](https://igvteam.github.io/igv-reports/examples/example_tab.html))

```bash

Expand All @@ -178,7 +178,7 @@ create_report test/data/variants/SKBR3_Sniffles_sv.vcf \

```

#### Create a structural variant report from a bedpe file with two locations (BEDPE format): ([Example output](https://igv.org/igv-reports/examples/1.9.0/example_bedpe.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

Expand All @@ -189,7 +189,7 @@ create_report test/data/variants/SKBR3_Sniffles_tra.bedpe \
--output example_bedpe.html
```

#### Create a report using a genome identifier: ([Example output](https://igv.org/igv-reports/examples/1.9.0/example_genome.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 \
Expand All @@ -200,7 +200,7 @@ create_report test/data/variants/variants.vcf.gz \
--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://igv.org/igv-reports/examples/1.9.0/example_config.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 \
Expand All @@ -212,7 +212,7 @@ create_report test/data/variants/variants.vcf.gz \
--output example_config.html
```

#### Create a variant report with custom ID link urls: ([Example output](https://igv.org/igv-reports/examples/1.9.0/example_idlink.html))
#### Create a variant report with custom ID link urls: ([Example output](https://igvteam.github.io/igv-reports/examples/example_idlink.html))

```bash

Expand All @@ -225,7 +225,7 @@ create_report test/data/variants/1kg_phase3_sites.vcf.gz \

```

#### Create a junction report from a splice-junction bed file: ([Example output](https://igv.org/igv-reports/examples/1.9.0/example_junctions.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 \
Expand Down Expand Up @@ -258,7 +258,7 @@ create_report test/data/wig/regions.bed \

```

#### Use of ```info-columns-prefixes``` option. Variant track only, no alignments. ([Example output](https://igv.org/igv-reports/examples/1.9.0/example_ann.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 \
Expand Down

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