VCFv4.5 Specification Inaccuracy -- Large Insertions (Circular) [§5.4.2]
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Open VCFv4.5.tex at lines 1512-1518 and compare the circular contig example with the MATEID definition and preceding insertion examples. Verify the four reciprocal pairings and confirm that all records retain EVENT=INS0; done means the example no longer self-references or points to the undefined bnd_C.
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Description
I think there may be a few MATEID typos in the circular contig example in VCF v4.5 (§5.4.2). (LaTeX Lines 1512-1518)
The example currently contains:
bnd_U ... MATEID=bnd_U
bnd_V ... MATEID=bnd_V
bnd_X ... MATEID=bnd_Y
bnd_Y ... MATEID=bnd_C
The first two appear to self-reference, and bnd_C is not defined in the example.
Based on the definition of MATEID (“ID of mate breakend”), the reciprocal pairing used in the preceding insertion examples, and the breakend topology shown here, I believe the intended values may be:
bnd_U ... MATEID=bnd_V
bnd_V ... MATEID=bnd_U
bnd_X ... MATEID=bnd_Y
bnd_Y ... MATEID=bnd_X
with all four records continuing to share EVENT=INS0.
Could you confirm whether these are typos in the current specification example? If so, I’d be happy to submit a small PR correcting the table.
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