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haploxt is a C/C++ software developed by [https://www.sph.umich.edu/csg/yli/ Yun Li] and [https://www.sph.umich.edu/csg/abecasis/ Goncalo Abecasis]. It calculates LD (D' and r<sup>2</sup>) from phased haplotypes.
haploxt is a C/C++ software developed by [https://www.sph.umich.edu/csg/yli/ Yun Li] and [https://www.sph.umich.edu/csg/abecasis/ Goncalo Abecasis]. It calculates LD (D' and r<sup>2</sup>) from phased haplotypes.
= Input Files =
== Required ==
=== Haplotype File ===
The input haplotype file is in the form of one haplotype per line (no delimiter between alleles). The file could contain fields other than the actual haplotypes but must proceed the actual haplotype field.
Sample haplotype file 1:
Indiv1 HAPLO1 142344111132344413444421333122313342113321324233112323134222
Indiv1 HAPLO2 144222444221443323334431431242131234311333144223411321334422
Indiv2 HAPLO1 144224441221443323334331431243131232311321123323432321334412
Indiv2 HAPLO2 342222444221344312343433333122313344113321324223112323334412
Sample haplotype file 2:
142344111132344413444421333122313342113321324233112323134222
144222444221443323334431431242131234311333144223411321334422
144224441221443323334331431243131232311321123323432321334412
342222444221344312343433333122313344113321324223112323334412
= Options =
= Options =
