Tools built with vcfpp If you have vcfpp.h and htslib installed in your system , then you can compile all the command line tools just by make -j4 otherwise, you need to specifiy the customized path make -j4 VCFPP=/path/to/vcfpp HTSINC=/path/to/htslib/header HTSLIB=/path/to/htslib/libray Syllable PBWT supports compressed VCF/BCF SyllablePBWT.cpp Convert VCF/BCF to BEAGLE file vcf2beagle.cpp Create DS tag for diploid samples given GP or GT tag vcf_addDS.cpp Swap REF and ALT and flip corresponding genotypes vcf_flipGT.cpp Increment POS for duplicated sites vcf_dupPos.cpp Remove sites with duplicated POS vcf_rmdupPos.cpp Report multiallelics vcf_multiallelics.cpp