hall-lab / svtyper

Bayesian genotyper for structural variants
MIT License
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Can I use svtyper to genotype Hydra output? #87

Closed jiangyuanluo closed 6 years ago

ernfrid commented 6 years ago

You would need to convert Hydra output to a VCF before trying to use SVTyper. It looks like bcbio has a conversion script here: https://github.com/bcbio/bcbio-nextgen/blob/master/scripts/utils/hydra_to_vcf.py

I can't guarantee that all necessary fields are present, but it looks likely to be close to generating a suitable input file (please see #64 for a list of required fields). Note that SVTyper only operates well on one sample at a time so if you have multiple samples you will need to run SVTyper individually for each sample.