diff --git a/README.md b/README.md index a83b8dd..b46d77a 100644 --- a/README.md +++ b/README.md @@ -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. @@ -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. @@ -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).