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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 =
= Input Files =
== Required ==
Sample haplotype file 2:
=== Haplotype File ===
142344111132344413444421333122313342113321324233112323134222
144222444221443323334431431242131234311333144223411321334422
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.<br><br>
144224441221443323334331431243131232311321123323432321334412
342222444221344312343433333122313344113321324223112323334412
Sample haplotype file 1:<br>
Indiv1 HAPLO1 142344111132344413444421333122313342113321324233112323134222<br>
Indiv1 HAPLO2 144222444221443323334431431242131234311333144223411321334422<br>
Indiv2 HAPLO1 144224441221443323334331431243131232311321123323432321334412<br>
Indiv2 HAPLO2 342222444221344312343433333122313344113321324223112323334412<br>
Sample haplotype file 2:<br>
142344111132344413444421333122313342113321324233112323134222<br>
144222444221443323334431431242131234311333144223411321334422<br>
144224441221443323334331431243131232311321123323432321334412<br>
342222444221344312343433333122313344113321324223112323334412<br>
= Options =
= Options =
(1) SNP : SNP name
(1) SNP : SNP name
(2) gErr : genotypic discordance rate
(3) aErr : allelic discordance rate
(4) matchedG : number of genotypes matched
(5) matchedA: number of alleles matched
(6) maskedG: total number of genotypes evaluated/masked (<=n of course) (I should change the naming to comparedG or evaluatedG)
<br>
<br>
(7) hetAerr : allelic discordance rate among heterozygotes
(7) hetAerr : allelic discordance rate among heterozygotes
(8) AL1: allele 1 (an arbitrary allele)
(9) AL2: allele 2
(10) freq1: frequency of AL1
(11) MAF
(12) #true 1/1: # individuals with experimental genotype AL1/AL1
(13) mm1/2: # of true AL1/AL1 being imputed as AL1/AL2
(14) mm2/2: # of true AL1/AL1 being imputed as AL2/AL2
(15) #true 1/2
(16) mm1/1
(17) mm2/2
(18) #true 2/2
(19) mm1/1
(20) mm1/2
<br>
<br>
(A) almajor: major allele
(A) almajor: major allele
(B) alminor: minor allele
(C) freq1: major allele frequency
(D) accuracy11: allelic concordance rate for homozygotes major allele
(E) accuracy12: allelic concordance rate for heterozygotes
(F) accuracy22: allelic concordance rate for homozygotes minor allele
<br>
<br>
(1) famid
(1) famid
(2) subjID
(3) gErr
(4) aErr
(5) matchedG
(6) matchedA
(7) maskedG
<br> This --byPerson option is useful if there is potential sample swap or inter-individual difference, e.g., sequencing depth, number of markers genotyped.
<br> This --byPerson option is useful if there is potential sample swap or inter-individual difference, e.g., sequencing depth, number of markers genotyped.
