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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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[chr10:93279155-94722587][DUP][SVLEN=1443432bp] #224

Open jzook opened 1 month ago

jzook commented 1 month ago

chr10 93279155 Minda_12 N <DUP> . PASS SVLEN=1443432;SVTYPE=DUP;SUPP_VEC=PB_severus_DUP827,PB_r_49,ONT_severus_DUP880,ONT_r_32,ILL_MantaDUP:TANDEM:172346:0:1:0:0:0,PB_ID_18116_2,ILL_1079034284:2,ILL_gridss177bf_181h,PB_Sniffles2.DUP.32AM9,ONT_ID_47785_2

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr10:93279155#ribbon

Maryamjehangir77 commented 3 weeks ago

This appears to be a tandem duplication, likely located within a region of loss of heterozygosity (LOH), as suggested by the 120x coverage detected via SplitThreader. The correct position of the left-side breakpoint is consistently observed at chr10:93,279,156 across all reads, while the right-side breakpoint is at chr10:94,722,587.

Screenshot 2024-10-07 at 11 52 08 AM

Screenshot 2024-10-07 at 11 47 01 AM

Screenshot 2024-10-07 at 11 48 43 AM

Left-side breakpoint

Screenshot 2024-10-07 at 12 22 22 PM

Right-side breakpoint

Screenshot 2024-10-07 at 12 29 39 PM