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  • Genomic coordinates in the BioNano VCF (OGM)

    Hi! I need a help with BioNano files.

    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 has provided field with link to UCSC with another coordinates.

    For example:

    Column POS and field END contain "chr4:88858934-88862760" and boundary error +-5991 bp

    But UCSC is "chr4:88852942-88868750"

    Which coordinates better for using? And why the results are so different?

    P.S: UCSC coordinates don't always match with POS/END -+ CIPOS/CIEND, sometimes they even haven't intersections
    ​
    Last edited by AviShn; 06-08-2024, 11:38 PM.

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