gCNV bugfix - make variant IDs unique #589
Merged
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Test batch: https://batch.hail.populationgenomics.org.au/batches/431755
Weird unforeseen issue here - When passing the VCF through SVAnnotate in GATK all the DEL variants were being removed. It seems to be that GATK-SV includes some weird semi-manual VCF parsing/translation to BED which retains only unique variant IDs...
CHR POS ID DEL,DUP ...
, i.e. each span is called as DUP and DEL on the same row, sharing a single IDThis change introduces an additional amendment in the VCF; the ID is edited to be
ID_ALT
- these values become unique in the whole dataset, and annotation now completes with both variant types retained