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lh3 / bgt

Flexible genotype query among 30,000+ samples whole-genome
MIT License
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Import VCF into existing bgt file #11

Closed sndrtj closed 7 years ago

sndrtj commented 7 years ago

Is there any way to import a VCF containing additional samples into an existing bgt file?

I've tried bgt import -S prefix.bgt 1.vcf followed by bgt import -S prefix.bgt 2.vcf, but this only seems to overwrite the existing file.

lh3 commented 7 years ago

Sorry. It is not possible to achieve that with bgt. You have to merge VCF files first (e.g. with GATK or bcftools) and then import the merged file.