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chore: header fixup
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clintval committed Jul 23, 2024
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Expand Up @@ -34,7 +34,7 @@ These tools are not meant to be used as a structural variant calling toolchain i
> [!IMPORTANT]
> All point intervals (1-length) reported by this toolkit are 1-based inclusive from the perspective of the reference sequence unless otherwise documented.
### `fgsv SvPileup`
### `SvPileup`

Collates pileups of reads over breakpoint events.

Expand All @@ -58,7 +58,7 @@ This process creates a collection of candidate breakpoint locations.

The tool outputs a table of candidate breakpoints and a BAM file with each alignment tagged with the ID of the breakpoint it supports (if any).

### `fgsv AggregateSvPileup`
### `AggregateSvPileup`

Aggregates and merges pileups that are likely to support the same breakpoint.

Expand All @@ -82,7 +82,7 @@ One shortcoming of the existing behavior, which should be corrected at some poin

The tool outputs a table of aggregated breakpoints and a modified copy of the input BAM file where each alignment is tagged with the ID of the aggregate breakpoint it supports (if any).

### `fgsv AggregateSvPileupToBedPE`
### `AggregateSvPileupToBedPE`

Converts the output of `AggregateSvPileup` to the [BEDPE format](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format).

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