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ARC-SV v0.9.6

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@jgarthur jgarthur released this 12 Aug 02:02
· 15 commits to master since this release

NOTE: VCF output is significantly different now, and a len_affected column has been added to arcsv_out.tab output.

Updates mostly related to somatic SV calling.

  • More tags in VCF output, including AF (allele fraction, for somatic calling). The VCF output should now be basically equivalent to the arcsv_out.tab output.
  • You can now do haploid-only calling with the option -f “”
  • Reference and gap files are now required arguments
  • added output of affected reference length (len_affected, or EVENT_AFFECTED_LEN in VCF), which for complex SVs may differ from the naively computed size as distance from first to last breakpoint
  • the --min_size option in filter-merge now uses the 'len_affected' column rather than the span of the SV; this is so, e.g., very small non-tandem duplications are still filtered appropriately.
  • Renamed options in filter-merge for readability, and added options useful for somatic SV calling.