Detecting compound heterozygous

Question

[_quantum_girl_]

I'd like to know if my variants are in cis or trans. How can I detect these compound heterozygous individuals? Which tools do you recommend?

[Pierre Lindenbaum]

you need a phased VCF.

if your vcf is not phased there are some tools that can be of help: SHAPEIT, Beagle, etc...

[_quantum_girl_]

I already have phased VCF. I guess my question was how to narrow them down to a list of variants. And then obtain haplotypes like this:

allele1=01000100111010001
allele2=10110010001000010

Where 0 is ref and 1 is alt.

I've recently read you can do these with bcftools, just wanted to know if there were other tools out there.