Structural variants in KOLF2.1J iPSCs using PacBio HiFi sequencing

Summary LongRead PacBio HiFi Sequenceing KOLF2.1J iPSC Cell line T2T-CHM13v2 and GRCh38 were used as the reference pav (v2.4.6) was used to call deletions, inversion, and insertion delly (v1.2.9) was used to call duplications SV smaller than 2,000 bp were filtered TRF was run on the sequences column TRF = YES : >=90% of the sequence was made up of TR column TRF = NO : <90% of the sequence was made up of TR SVs were intersected with SD annotations from UCSC ( bedtools intersect 90% overlap) column SD = YES : >=90% of the SV overlapped SD region column SD = NO : <90% of the SV overlapped SD region for insertions, the YES or NO is indicative of whether the SV was within the SD region or not (no overlap)