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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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[chr19:39706584-50554250][DEL][SVLEN=10847666bp] #279

Open jzook opened 2 weeks ago

jzook commented 2 weeks ago

chr19 39706584 Minda_67 N <DEL> . PASS SVLEN=10847666;SVTYPE=DEL;SUPP_VEC=PB_severus_DEL3306,PB_r_198,ONT_severus_DEL3735,ONT_ID_51104_2,ONT_r_120,ILL_MantaDEL:247507:0:1:0:0:0,PB_ID_62347_2,ILL_1605497385:2,ILL_gridss269fb_11920h,PB_Sniffles2.DEL.20CM12,ONT_Sniffles2.DEL.21CM12

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr19:39706584#ribbon

jmcdani commented 1 week ago

Appears to be true large (10MB) DEL with exact breakpoint although % of reads supporting DEL differ.
contains smaller SVs #280 and #281 Screenshot 2024-10-17 at 3 43 41 PM Screenshot 2024-10-17 at 3 44 29 PM

Left breakpoint appears exact with left alignment, with supplementary reads mapping mapping to right breakpoint +1 Deletion in LGALS14 gene Screenshot 2024-10-17 at 3 55 44 PM

Right breakpoint appears exact with left alignment, with supplementary reads mapping mapping to right breakpoint +1 Deletion in LRRC4B gene Screenshot 2024-10-17 at 3 58 10 PM

Smaller fraction of reads support deletion at left breakpoint (~18% PB, ~30% ONT, ~19% element) Approximately half reads support DEL with all techs at right breakpoint Screenshot 2024-10-17 at 4 10 17 PM This is likely associated with overlapping variants in this region Screenshot 2024-10-17 at 4 23 59 PM