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
1 stars 0 forks source link

[chr7:6408188-6408254][DEL][SVLEN=66bp] #202

Open jzook opened 1 month ago

jzook commented 1 month ago

chr7 6408188 Minda_132 N <DEL> . PASS SVLEN=66;SVTYPE=DEL;SUPP_VEC=PB_d_403,ONT_d_185,ILL_MantaDEL:125544:0:0:0:0:0,PB_ID_25665_2,ONT_ID_40016_2,ILL_2186766853:2,PB_Sniffles2.DEL.C2M6,ONT_Sniffles2.DEL.C3M6,PB_severus_DEL6581,ONT_severus_DEL7572

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr7:6408188#ribbon

aysegokce commented 1 month ago

Small deletion Looks like clonal but there are spanning reads There is a nearby deletion SVLen = 63 BP1 = 6408191

Screenshot 2024-10-07 at 3 39 10 PM Screenshot 2024-10-07 at 3 31 23 PM Screenshot 2024-10-07 at 3 32 17 PM
jzook commented 1 month ago

It looks to me like this is in the same subclone that the nearby del #201 is in, and also doesn't seem to be in a TR but is in a SINE?

Screenshot 2024-10-07 at 10 07 50 PM