diff --git a/README.md b/README.md index f9f381f..01d980c 100644 --- a/README.md +++ b/README.md @@ -84,7 +84,7 @@ The tool outputs a table of aggregated breakpoints and a modified copy of the in ## `AggregateSvPileupToBedPE` -Convert the output of `AggregateSvPileup` to BEDPE. +Converts the output of `AggregateSvPileup` to the [BEDPE format](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format). ```console fgsv AggregateSvPileupToBedPE \ @@ -92,7 +92,7 @@ fgsv AggregateSvPileupToBedPE \ --output sample.svpileup.aggregate.bedpe ``` -The tool [`fgsv AggregateSvPileupToBedPE`](https://github.com/fulcrumgenomics/fgsv/blob/main/docs/tools/AggregateSvPileupToBedPE.md) is used to convert the output of `AggregateSvPileup` to the [BEDPE format](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format) so that it can be viewed in [IGV](https://igv.org/) and other BEDPE-supporting genome browsers. +The tool [`fgsv AggregateSvPileupToBedPE`](https://github.com/fulcrumgenomics/fgsv/blob/main/docs/tools/AggregateSvPileupToBedPE.md) is used to convert the output of `AggregateSvPileup` to BEDPE so that it can be viewed in [IGV](https://igv.org/) and other BEDPE-supporting genome browsers. For example: ![BEDPE in IGV](docs/img/fgsv-bedpe.png)