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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Vcf format #194

Closed gmykim closed 3 years ago

gmykim commented 3 years ago

I'm wondering if I could get a clarification on the vcf output format. I need the SVTYPE (specifically deletion) and the End positions that correspond to the start position (thus giving me the length of the SV).

Thanks in advance!

dancooke commented 3 years ago

Octopus doesn't report symbolic SV variants - all variants are reported as "SNPs and small indels" (section 5.2 of VCF 4.3 spec).