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docs: little fixup
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clintval committed Jul 23, 2024
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Expand Up @@ -84,15 +84,15 @@ 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 \
--input sample.svpileup.aggregate.txt \
--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)

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