Genomic coordinates in the BioNano VCF

Question

[avigail.shnaider]

Hi! I have a VCF file with structural variants from the BioNano, there are computed approximate genomic coordinates of structural variant in column POS and field END. But also the file has the field with link to UCSC with another coordinates. For example

POS and END: chr4:88858934-88862760 and error +-5991 bp

But UCSC is chr4:88852942-88868750

Which coordinates better for using?

Answer 1

[cmdcolin]

the ucsc link appears to include the error size subtracted from the start and added to the end

[avigail.shnaider]

it is clear, but UCSC coordinates don't always match with POS/END +- CIPOS/CIEND, sometimes they even haven't intersections

[cmdcolin]

can you post examples of those? i'd suggest posting the entirety of vcf data line(s) if possible