vcftools/ plink conserve phase information

Question

[Wietje]

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!

Answer 1

[chrchang523]

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

Have you tried bcftools?

[Wietje]

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