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How to convert a VCF file to a this format? #219

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guojingfang123 opened this issue Jan 16, 2020 · 1 comment

guojingfang123 commented Jan 16, 2020

Hi, I only have VCF files now, how can I change it to the format "master_pinus_data_genotype.txt"? Are there tools or scripts? Thank you.

Contributor

zkamvar commented Jan 16, 2020

Hello,

If you have VCF data, {pegas} can import it with read.vcf: https://www.rdocumentation.org/packages/pegas/versions/0.12/topics/read.vcf, which gets stored as a "loci" object. You can also use {vcfR} with read.vcrR: https://www.rdocumentation.org/packages/vcfR/versions/1.8.0/topics/VCF%20input%20and%20output and then you can use vcfr2genind to import your data to genind format: https://knausb.github.io/vcfR_documentation/export_genind_genclone.html

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