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@d-cameron d-cameron released this 22 Sep 06:17
· 965 commits to master since this release
v2.0.0
6823a9d

GRIDSS output now includes the reporting of single breakends. When the breakpoint sequence is novel or multi-mapping on one side, an unambiguous breakpoint call cannot be made as only one side of the breakpoint is uniquely mappable. In such cases GRIDSS will now call a single breakend. See section 5.4.9 of the VCF file format specifications document for details on how single breakends are represented in VCF.

  • Single breakend are now included in the default output VCF
  • The command-line tool gridss.AnnotateUntemplatedSequence can be used to identify potential partner breakends both in the reference genome, and against other reference databases (such as viral databases for the identification of integrated DNA virus).

This release also includes the following bug fixes:

  • #174 Reporting no inexact homology when a misalignment of the flanking sequence is detected
  • #174 No longer reporting negative inexact homology when untemplated inserted sequence is present
  • #172 BANRPQ and BANSRQ headers were set to Integer when values were actually Float
    • Fixes crash when using GRIDSS with bcftools

Note: Due to their nature, single breakend calls have a higher false positive rate than breakpoint calls. Furthermore, due to the nature of read mapping, single breakends calls are enriched in low complexity sequence such as micro-satellites. Although there are many true positives, the false positive rate in these regions is higher for all general purpose SV callers such as GRIDSS.

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