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jzook / testHG008curation

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[chr9:22631432-22939871][DUP][SVLEN=308438bp] #91

Open jzook opened 1 week ago

jzook commented 1 week ago

chr9 22631432 Minda_146 N <DUP> . PASS SVLEN=308438;SVTYPE=DUP;SUPP_VEC=ILL_MantaDUP:TANDEM:154784:0:1:0:0:0,ILL_gridss156bf_714h,PB_severus_DUP7420,ONT_severus_DUP8542,PB_ID_34921_2,ILL_2280402139:2,PB_r_336,ONT_r_227,PB_Sniffles2.DUP.79M8,ONT_ID_54325_2,ONT_Sniffles2.DUP.7EM8

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr9:22631432#ribbon

jzook commented 5 days ago

DUP appears to be clearly supported by coverage and reads

Screenshot 2024-09-16 at 10 20 18 PM Screenshot 2024-09-16 at 10 21 14 PM

increased coverage goes from 22631433-22939870 or 22631435-22939872 (due to 2bp homology). Need to figure out how to represent this in vcf

Screenshot 2024-09-16 at 10 37 58 PM Screenshot 2024-09-16 at 10 43 29 PM

It also appears to be in all the cells since it roughly doubles coverage in a region that has LOH, though hard to know for certain without single cell data