ALT coordinate

[uretaj]

Hi,

How is the coordinate in the ALT field calculated? I noticed that for some SVs it's the start position of the partner + 1 while for others it's just the start position. Does the calculation change based on whether there's uncertainty around the breakend location or not?

[d-cameron]

GRIDSS uses VCF breakpoint notation (See section 5.4 of https://samtools.github.io/hts-specs/VCFv4.5.pdf).

If you have an example where you think GRIDSS deviates from the VCF specs, please post it here so I can see if it's just VCF being hard to interpret, or an actual issue with GRIDSS output.

Does the calculation change based on whether there's uncertainty around the breakend location or not?

No, but GRIDSS does use centre-alignment as the nominal calling position for both imprecise variants and variants with breakpoint microhomology. It's possible that there's an off-by-one bug where the left and right breakends are reporting different nominal centre-aligned position when the homolgy length is even.