[Vcftools-help] Phased missing data issue for recode vcf

[Kelley, J. <joa...@ws...>]

I have a vcf with phased missing data (.|.) presumably because of the GATK Haplotype Caller. When I filter with vcftools and recode the output vcf has only . for the genotype, which throws an error for other programs.

Any ideas how to solve this?

Thanks!

Joanna L. Kelley, PhD
Associate Professor, School of Biological Sciences
Washington State University
joa...@ws...<mailto:joa...@ws...>
509-335-0037
http://labs.wsu.edu/genomes