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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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[chr6:70580536-70708185][DUP][SVLEN=127649bp] #189

Open jzook opened 2 months ago

jzook commented 2 months ago

chr6 70580536 Minda_119 N <DUP> . PASS SVLEN=127649;SVTYPE=DUP;SUPP_VEC=ILL_MantaDUP:TANDEM:116200:0:1:0:0:0,ILL_gridss113bf_4050h,PB_severus_DUP6199,ONT_severus_DUP7149,PB_ID_42846_2,ILL_2591031218:2,PB_r_296,ONT_r_194,ONT_ID_67243_2,PB_Sniffles2.DUP.23DM5,ONT_Sniffles2.DUP.25FM5

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr6:70580536#ribbon

aquaskyline commented 1 month ago

A correct tandem duplication with a seemingly correct 90bp DEL ~#191~ #190 in it. Dragen called the DUP as well. DUP happens in about half of the reads in a single phase (phase 2 in PB reads).

Screenshot 2024-10-05 at 23 22 35 Screenshot 2024-10-05 at 22 11 11 Screenshot 2024-10-05 at 22 11 19

Screenshot 2024-10-06 at 12 41 31

Left-end breakpoint Screenshot 2024-10-06 at 12 42 36

Right-end breakpoint Screenshot 2024-10-06 at 12 43 43

jzook commented 1 month ago

ah, I think you meant #190 instead

aquaskyline commented 1 month ago

ah, I think you meant #190 instead

That's correct. Updated.