[chr2:128153403-128332892][DUP][SVLEN=179488bp]

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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[chr2:128153403-128332892][DUP][SVLEN=179488bp] #102

Open jzook opened 1 month ago

jzook commented 1 month ago

chr2 128153403 Minda_78 N <DUP> . PASS SVLEN=179488;SVTYPE=DUP;SUPP_VEC=PB_severus_BND3745_2,PB_r_226,ONT_severus_DUP4249,ONT_r_136,ILL_MantaDUP:TANDEM:41141:0:1:0:0:0,ONT_ID_35717_2,ILL_3012671302:2,ILL_gridss37bf_12909h,PB_ID_23797_2,PB_Sniffles2.DUP.3A4M1,ONT_Sniffles2.DUP.3B7M1

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr2:128153403#ribbon

nate-d-olson commented 1 month ago

No similar SVs within a few kb: nothing in MINDA large variants list, don't see any other variants when zoomed out in IGV
- Breakpoints appear correct: IGV screenshots
I don't believe it is a translocation (not sure what to look for)
Unclear variant frequency
- About half PacBio and ONT reads support variant
- PacBio phasing questionable: 3/4 of reads assigned to Hap1, 1/4 to Hap2, and about half hap1 reads support duplication

Other Ribbon/ Split threader images of the variant