I have a phased genotype VCF file(i.e haplotype in vcf format). I am interested only in the haplotypes that are there in phased vcf file. Please help or suggest some other way to do it. 
Hello siddazra,

does [bcftools convert][1] with the `--hapsample` option do what you want?

Other solution is mention in this [thread][2].

fin swimmer


  [1]: http://www.htslib.org/doc/bcftools.html#convert
  [2]: https://www.biostars.org/p/292843/