I am using Eage to phase plink input. I maintain --keep-allele-order throughout my workflow. Eagle outputs .haps (Oxford phased haplotype file), which I convert to VCF with shapeit. I did some sanity checks and find that this process reverses REF/ALT designation and genotypes for every single one of my snps and indels. Comparing alt allele frequency to reference strongly suggests that I do not have a build issue, so the workaround was initially to do
bcftools norm --check-ref -s -f hg19.fa input.vcf > output.vcf
to flip everything back after converting to vcf with shapeit, which perfectly flips every single one of my snps, but does not seem to do the same for indels. Is there a way to do this for indels as well. My alternative thought is just to use bcf as input for eagle, which should avoid the Plink/Oxford formats completely.