Open jzook opened 4 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).
looks exactly correct in dragen based on concordance with assembly ins length. also in all reads from hap1 in HiFi so likely clonal
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