[chr2:89324416-89324416][BND][JoinedTo=chrX:8495890]]

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

[chr2:89324416-89324416][BND][JoinedTo=chrX:8495890]] #101

Open jzook opened 2 months ago

jzook commented 2 months ago

chr2 89324416 Minda_77 N N]chrX:8495890] . PASS SVLEN=-1;SVTYPE=BND;SUPP_VEC=PB_severus_BND7803_1,ONT_severus_BND9049_1,PB_Sniffles2.BND.299M1,ONT_Sniffles2.BND.290M1,ONT_r_135_1,PB_ID_21706_2,ONT_ID_32479_2

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr2:89324416#ribbon

nate-d-olson commented 2 months ago

No similar SVs within few kbs but 148bp deletion in chrX at end of BND.
Breakpoints: appear correct, with most reads supporting defined breakpoints with fewer reads supporting other positions.
I think this is a translocation, but does not cause a CNA
Variant frequency unclear - present in all cells, heterozygous variant

jzook commented 1 month ago

complex translocation breakpoint on chrX related to #294 so will need more investigation. Also near gap near centromere in chr2