[chr7:6404812-6406029][DEL][SVLEN=1217bp]

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

[chr7:6404812-6406029][DEL][SVLEN=1217bp] #201

Open jzook opened 1 month ago

jzook commented 1 month ago

chr7 6404812 Minda_131 N <DEL> . PASS SVLEN=1217;SVTYPE=DEL;SUPP_VEC=PB_ID_25664_2,PB_d_402,ONT_ID_40015_2,ONT_d_184,ILL_MantaDEL:2:37144:37145:0:1:0,PB_severus_DEL6580,ONT_severus_DEL7571,PB_Sniffles2.DEL.C3M6,ONT_Sniffles2.DEL.C4M6,ILL_1528590481:2,ILL_gridss123fb_23891h

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr7:6404812#ribbon

aysegokce commented 1 month ago

Look real. Exact breakpoints Looks like clonal but there are spanning reads. Does not appear in the assembly. Nearby deletion.

jzook commented 1 month ago

@aysegokce I think this is subclonal since it is only in a fraction of the HiFi hap1 reads and some reads span the deletion and don't have the smaller del from the other haplotype. Also, this isn't annotated as a TR but does fall in a region with SINEs. Am I missing something?