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

[chr17:32305444-32673231][BND][JoinedTo=chr17:32673230]] #265

Open jzook opened 1 month ago

jzook commented 1 month ago

chr17 32305444 Minda_53 N N]chr17:32673230] . PASS SVLEN=367786;SVTYPE=BND;SUPP_VEC=PB_severus_INV2749,ONT_severus_INV3110,PB_ID_32705_2,PB_r_168_1,PB_Sniffles2.INV.1C7M10,ONT_ID_61071_2,ONT_r_103_1,ONT_Sniffles2.INV.1FBM10,ILL_3070698818:2,ILL_gridss252bb_1931h,ILL_MantaBND:32460:1:2:0:0:0:0

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr17:32305444#ribbon

aganezov commented 1 month ago

Appears to be a apart of a relatively complex rearrangement. Related / overlaps with #266
Zoomed-out signature of coverage suggests a duplication-like event, but the read alignment orientation disagrees with such simplistic discription.

Screenshot 2024-10-11 at 10 28 21

Screenshot 2024-10-11 at 10 29 55

Left breakpoint is exact across all technologies and assmebly and is at chr17:32,305,444

Screenshot 2024-10-11 at 10 34 41

The rearrangement only affect one haplotype, as the overall region is an LOH (see haplotype-specific HP2 insertion in normal and all-read supporting insertion in tumor).

Screenshot 2024-10-11 at 10 35 16

Right breakpoint of this junction appears to be exact at chr17:32,673,230.

Screenshot 2024-10-11 at 10 39 06