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Genomic coordinates in the BioNano VCF

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?

bionano vcf smap optical_genome_mapping
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updated by cmdcolin cmdcolin • written by avigail.shnaider • avigail.shnaider

1 answer

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

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written by cmdcolin cmdcolin

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

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written by avigail.shnaider • avigail.shnaider

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

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written by cmdcolin cmdcolin

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