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.