[chr8:104941340-104941723][INS][SVLEN=383bp]

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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[chr8:104941340-104941723][INS][SVLEN=383bp] #213

Open jzook opened 4 weeks ago

jzook commented 4 weeks ago

chr8 104941340 Minda_143 N <INS> . PASS SVLEN=383;SVTYPE=INS;SUPP_VEC=ONT_severus_INS20820,ONT_Sniffles2.INS.2BAM7,PB_severus_INS18348,PB_i_826,ONT_i_332,PB_Sniffles2.INS.296M7,PB_ID_47897_1,ONT_ID_24344_1

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr8:104941340#ribbon

jo-mc commented 3 weeks ago

This is a truncated and five prime inverted Line1 insertion. Insertion of line1 position 6054 - 5792 followed by inverted line 1 position 5665 – 5778 with a target site duplication of CATAGTTACTTTTA. There is no transducted sequence, source Line1 could be from multiple locations. Present in Illumina tumour, absent in Revio and Illumina normal. Dragen VCF shows the insert as well. Concordance with reference L1HS: one SNP variation (of available sequence).

jzook commented 3 weeks ago

looks exactly correct in dragen based on concordance with assembly ins length. also in all reads from hap1 in HiFi so likely clonal