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vcftools/ plink conserve phase information

Hello fellow Biostars,

I would like to extract a set of samples from a very large VCF file that already contains phase information. However, when I extract individuals with the option --keep in either PLINK or vcftools, the phase information is lost in the new subset. Is there a way to avoid this/ conserve the phase?

All help is heartily appreciated!

vcftools phase information haplotype plink
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updated by chrchang523 chrchang523 • written by Wietje Wietje

1 answer

plink 2.0 can do this, but you may still lose some other types of information in the VCF.

Have you tried bcftools?

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written by chrchang523 chrchang523

Yes, I switched to bcftools for tha t- and vcf-subset also seems to do the job - thanks for the idea though!

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written by Wietje Wietje

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