[chr10:67470511-68211500][BND][JoinedTo=chr10:68211499]]

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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[chr10:67470511-68211500][BND][JoinedTo=chr10:68211499]] #223

Open jzook opened 2 weeks ago

jzook commented 2 weeks ago

chr10 67470511 Minda_11 N N]chr10:68211499] . PASS SVLEN=740988;SVTYPE=BND;SUPP_VEC=ILL_MantaDUP:TANDEM:170154:0:1:0:0:0,ILL_gridss174bf_4460h,PB_severus_BND783_2,ONT_severus_BND834_2,ILL_2795390560:2,PB_r_45,ONT_r_30,PB_ID_18113_2,ONT_ID_47780_2

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr10:67470511#ribbon

Maryamjehangir77 commented 1 week ago

The tandem duplication exhibits additional variants within the duplicated copies.
Breakpoints differ between sequencing technologies: in ONT and Illumina data, the breakpoints are slightly shifted, whereas in HiFi reads, two distinct breakpoints are observed. This suggests a more complex structural rearrangement.

left breakpoint

right breakpoint

jzook commented 1 week ago

I think this is likely correctly described as a tandem dup in the dragen call in the sheet, and the difference in breakpoints is due to the sequence homology listed in the dragen call. so I made the dragen call green. Also, I think the nearby SNV is germline rather than somatic so I removed the additional small variants tag