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SRescue

A tool for validating short-read–specific SVs missed by long-read callers via breakpoint force-genotyping in long-read WGS data.

Details

Long-read SV callers may miss certain somatic SVs with low VAFs due to relatively lower sequencing coverage. In contrast, short-read SV detection often suffers from a high false-positive rate caused by mapping ambiguities and the lack of spanning-read evidence. To retrieve and validate the short-read–specific SVs that were missed by long-read callers, this tool was developed. The workflow is summarized as follows:

  1. Identify SVs detected exclusively by short-read callers,
  2. Convert the detected duplications into insertions, because the long-read force-genotyping tools typically have limited sensitivity for duplications,
  3. Use cuteSV to force-genotype the breakpoints of short-read-specific SVs in the long-read normal and tumor data,
  4. Retrieve short-read–specific SVs that have at least 1 supporting read in the long-read tumor sample and no supporting reads in the matching normal sample,
  5. Verify whether the retrieved duplications (represented as insertions in the callsets) are true duplications by comparing the supporting read sequences,
  6. Merge the long-read-specific, common, and validated short-read-specific SVs into the final SV set.

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Pipeline for SR-LR integration

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