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docs: do not repeat thyself
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clintval committed Jul 23, 2024
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Expand Up @@ -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.

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