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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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[chr22:49059745-49174454][DUP][SVLEN=114709bp] #293

Open jzook opened 1 month ago

jzook commented 1 month ago

chr22 49059745 Minda_93 N <DUP> . PASS SVLEN=114709;SVTYPE=DUP;SUPP_VEC=ILL_MantaDUP:TANDEM:261263:0:1:0:0:0,ILL_gridss287bf_1071h,PB_ID_55304_2,ONT_ID_65408_2,ILL_2329842478:2,PB_r_250,ONT_r_158,PB_Sniffles2.DUP.212M15,ONT_Sniffles2.DUP.229M15,PB_severus_DUP4523,ONT_severus_DUP5247

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr22:49059745#ribbon

vkpat commented 1 month ago

This appears to be duplication and likely clonal since the coverage is increasing from 100 ---> 200.

Screenshot 2024-10-21 at 1 12 07 PM Screenshot 2024-10-21 at 1 13 06 PM Screenshot 2024-10-21 at 1 22 27 PM Screenshot 2024-10-21 at 1 25 04 PM

Pacbio Revio appear to have the correct right breakpoint with the ATC homology sequence at the start however, ONT and element right breakpoint is 3 bp long Also, as seen in IGV, the Exact left breakpoint across ONT, Revio, and Element