[chr9:22631432-22939870][DUP][SVLEN=308438bp]

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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[chr9:22631432-22939870][DUP][SVLEN=308438bp] #216

Open jzook opened 1 month ago

jzook commented 1 month 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

chunlinxiao commented 1 month ago

This large DUP appears a true one in a region with ~200X, but the nearby and other region ~100X for tumor sample (tumor chr9 lost one copy by verkko), clearly supported by HiFi and ONT_UL. The predicted breakpoints are somewhat accurate, with 1 or2 bps off based on HiFi/ONT alignments. Now the DUP adjusted as chr9:22631433-22939872.

chunlinxiao commented 1 month ago

Ribbon evidence 1/2/3

chunlinxiao commented 1 month ago

IGV evidence 1/2/3

jzook commented 1 month ago

I think this is one of the tricky cases to get exact breakpoints due to sequence homology at the breakpoint, but I think if you take the leftmost alignment for both breakpoints (and have POS be the base before the breakpoint), you get the exact change in the dragen call and this one, so I reverted it back to its original values and made it green.