[chr20:40907241-40907338][DEL][SVLEN=97bp]

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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[chr20:40907241-40907338][DEL][SVLEN=97bp] #287

Open jzook opened 3 weeks ago

jzook commented 3 weeks ago

chr20 40907241 Minda_87 N <DEL> . PASS SVLEN=97;SVTYPE=DEL;SUPP_VEC=ONT_Sniffles2.DEL.20CM13,PB_ID_37586_2,PB_d_271,ONT_ID_26678_2,ONT_d_115,ILL_MantaDEL:252631:0:0:0:0:0,PB_severus_DEL4138,ONT_severus_DEL4737,ILL_2186766853:2,ILL_gridss275fb_11860h,PB_Sniffles2.DEL.1B3M13

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr20:40907241#ribbon

Maryamjehangir77 commented 2 weeks ago

This deletion appears to be a true event supported by both HiFi and ONT sequencing. The breakpoints are inconsistently defined, indicating a deletion ranging from 40907864 bps to 40907779 bps as observed on IGV. Present exclusively in one haplotype showing in hifi reads.

Screenshot 2024-10-15 at 4 23 34 PM

Left breakpoint

Right breakpoint