Improve CNV naming in REPORT
Background
Naming of CNVs in the REPORT is not ideal at the moment, and should be adapted to ISCN criteria. Example naming (according to ISCN):
- Breakpoints determined
seq[GRCh38] dup(8)(q24.21q24.21) NC_000008.11:g.128746677_128749160dup
- Breakpoints uncertain
seq[GRCh37] 14q31.3q32.33(83159163×2,85994993_104647150×3,104710536×2) NC_000014.8:g.(83159164_85994993)_(104647150_104710535)dup
Users are willing to perform some manual editing, but at a minimum need:
- Chromosome band(s): All cytobands that includes the CNV (1 bp minimum). Handled in #1969
- Correct HGVSg with chromosome contig reference instead of chr, e.g. NC_000012.11 for chr12 (where .11 is GRCh37)
- Genome build: GRCh37
Implementation
Write variants like this in the REPORT (assuming that breakpoints are determined):
seq[GRCh37] [dup/del]([chromosome number])([cytoband_start][cytoband_stop])
[HGVSg]
Notes:
- if only one cytoband affected, repeat in start/stop, e.g. "(q24.21q24.21)"
- Correcting HGVSg is defined in a separate issue: #2104 (closed)
Edited by Morten C. Eike