[chr14:102499943-102762793][DUP][SVLEN=262850bp]

jzook / testHG008curation

This repository is primarily for the Genome in a Bottle Consortium to curate structural variants in HG008

https://www.nist.gov/programs-projects/cancer-genome-bottle

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[chr14:102499943-102762793][DUP][SVLEN=262850bp] #253

Open jzook opened 1 month ago

jzook commented 1 month ago

chr14 102499943 Minda_41 N <DUP> . PASS SVLEN=262850;SVTYPE=DUP;SUPP_VEC=PB_severus_DUP2123,PB_r_97,ONT_r_81,ILL_MantaDUP:TANDEM:2:71784:71785:0:0:0,PB_ID_58650_2,ILL_225272706:2,ILL_gridss229bf_3708h,PB_Sniffles2.DUP.1D4MD,ONT_severus_DUP2337,ONT_ID_56209_2,ONT_Sniffles2.DUP.1CFMD

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr14:102499943#ribbon

d-cameron commented 1 month ago

Simple isolated tandem duplication
Final base of duplication is a germline SNV
- Some (short read) callers incorrectly report this event as 1bp smaller with a 1bp insertion at the breakpoint
Duplicates RCOR1 (oncogene), and ANKRD9 (tumour supressor)

Correct call has HOMSEQ=GT;CIPOS=0,2 (the SNV causes some callers to miss the homology call)