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clintval committed May 10, 2024
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Expand Up @@ -82,8 +82,8 @@ Convert the output of `AggregateSvPileup` to BEDPE.

```console
fgsv AggregateSvPileupToBedPE \
--input sample.svpileup.aggregate.txt \
--output sample.svpileup.aggregate.bedpe
--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. For example:
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