From 3f52590b0dd2752305ef089fa1ec40cbedc828e3 Mon Sep 17 00:00:00 2001 From: clintval Date: Mon, 12 Aug 2024 18:54:20 -0700 Subject: [PATCH] docs: suit review from @nh13 --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index b46d77a..6b5a88e 100644 --- a/README.md +++ b/README.md @@ -25,11 +25,11 @@ More detailed documentation can be found in the [docs folder](docs/01_Introducti ## Introduction to the `fgsv` Toolkit -The `fgsv` toolkit contains tools for effective structural variant debugging. -These tools are not meant to be used as a structural variant calling toolchain in-and-of-itself; instead, it is better to think of `fgsv` as an effective breakpoint detection and structural variant exploration toolkit. +The `fgsv` toolkit contains tools for effective structural variant investigation. +These tools are not meant to be used as a structural variant calling toolchain in-and-of-itself; instead, it is better to think of `fgsv` as a breakpoint detection and structural variant exploration toolkit. > [!NOTE] -> When describing structural variation, we use the term **breakpoint** to mean a junction between two loci and the term **breakend** to refer to one of the loci in a breakpoint. +> When describing structural variation, we use the term **breakpoint** to mean a junction between two loci and the term **breakend** to refer to one of the loci on one side of a breakpoint. > [!IMPORTANT] > All point intervals (1-length) reported by this toolkit are 1-based inclusive from the perspective of the reference sequence unless otherwise documented. @@ -45,7 +45,7 @@ fgsv SvPileup \ ``` The tool [`fgsv SvPileup`](https://github.com/fulcrumgenomics/fgsv/blob/main/docs/tools/SvPileup.md) takes a queryname-grouped BAM file as input and scans each query group (template) of alignments for structural variant evidence. -For a simple example: a paired-end read may have one alignment per read—one alignment for read 1 and another alignment for read 2 mapped to different reference sequences supporting a putative translocation. +For a simple example: a paired-end read may have one alignment per read (one alignment for read 1 and another alignment for read 2) mapped to different reference sequences supporting a putative translocation. Primary and supplementary alignments for a template are used to construct a “chain” of aligned sub-segments in a way that honors the sub-segments mapping locations and strandedness as compared to the reference sequence. The aligned sub-segments in a chain relate to each other through typical alignment mechanisms like insertions and deletions but also contain information about the relative orientation of the sub-segment to the reference sequence and importantly, jumps between reference sequences which could indicate translocations.