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atks / vt

A tool set for short variant discovery in genetic sequence data.
http://genome.sph.umich.edu/wiki/vt
MIT License
192 stars 3 forks source link

Can it call tetraploid variants? #89

Open afzm opened 6 years ago

atks commented 6 years ago

@afzm

no it does not, may I know what are you intending to use it for? e.g. the use case, the organism?

afzm commented 6 years ago

Thanks for answering, I am interested in calling variants on some tetraploid plants genomes, despite not being able to call the variants, can it normalize them if I pass it a .vcf?

atks commented 6 years ago

@afzm

it can normalize them. the concept of ploidy exists in the genotype fields, normalization just changes the REF and ALT fields.