diff --git a/README.md b/README.md index 87b49c6..f9f381f 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ 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. -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 in relation to the reference sequence. +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. See the [SAM Format Specification v1](https://samtools.github.io/hts-specs/SAMv1.pdf) for more information on how reads relate to alignments.