Haploxt

haploxt is a C/C++ software developed by Yun Li and Goncalo Abecasis. It calculates LD (D' and r²) from phased haplotypes.

Input Files

Required Input

Haplotype File

Fed to the option --haps or -h, 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. Allele coding is flexible: accepted coding includes 1234, ACGT, 12, AB etc.

Sample haplotype file 1:
Indiv1 HAPLO1 142344111132344413444421333122313342113321324233112323134222
Indiv1 HAPLO2 144222444221443323334431431242131234311333144223411321334422
Indiv2 HAPLO1 144224441221443323334331431243131232311321123323432321334412
Indiv2 HAPLO2 342222444221344312343433333122313344113321324223112323334412

Sample haplotype file 2:
142344111132344413444421333122313342113321324233112323134222
144222444221443323334431431242131234311333144223411321334422
144224441221443323334331431243131232311321123323432321334412
342222444221344312343433333122313344113321324223112323334412

SNP File

Fed to the option --snps or -s, the input SNP file is a list of SNP name in the same order as in the haplotype file. One SNP per line.

Sample SNP file:
SNP1
SNP2
SNP3
...

Options

--impped --impdat

specify one input pedigree set.

--trueped --truedat

specify the other input pedigree set.

--match

generates a matrix taking values 0,1,2 indicating # of matched alleles. The dimension of the matrix is # of overlapping individuals times # of overlapping markers of the two input pedigree sets.

--bySNP

is turned on by default to generate SNP specific measures. The output .bySNP will contain the following 6 fields for each SNP:

   (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)

--byGeno

can be added on top of --bySNP. It will generates the following fields after the 6 fields above:

   (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

--accuracyByGeno

Similar to --byGeno, it is used on top of --bySNP. It may be used together with --byGeno. It will generate the following fields, after (7-20) is --byGeno is turned on or after the 6th field otherwise.

   (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

--byPerson

generates a separate output file .byPerson and contains the following information for each person:

   (1) famid
 (2) subjID
 (3) gErr
 (4) aErr
 (5) matchedG
 (6) matchedA
 (7) maskedG

This --byPerson option is useful if there is potential sample swap or inter-individual difference, e.g., sequencing depth, number of markers genotyped.

--maskflag --maskped --maskdat

CalcMatch compares all genotypes overlapping the two input sets. However, when --maskflag is turned on AND --maskped and --maskdat are specified (I know ...) it compares only the following subset of the overlapping genotypes: genotypes either not found (i.e., individual or marker not included) or missing (included but with value 0/0, N/N, ./. etc) in --maskped / --maskdat. These options are useful when some individuals were masked for some SNPs while others masked for a different set of SNPs.

example command lines

 CalcMatch --trueped true.ped --truedat true.dat --impped imp.ped --impdat imp.dat -o CalcMatch.Output --byPerson 

Will generate CalcMatch.Output.bySNP (6 fields only) and CalcMatch.Output.byPerson.

 CalcMatch --trueped true.ped --truedat true.dat --impped imp.ped --impdat imp.dat -o CalcMatch.Output --byGeno --byPerson 

Will generate CalcMatch.Output.bySNP (6+20 fields) and CalcMatch.Output.byPerson.

 CalcMatch --trueped true.ped --truedat true.dat --impped imp.ped --impdat imp.dat -o CalcMatch.Output --accuracyByGeno --byPerson 

Will generate CalcMatch.Output.bySNP (6+6 fields only) and CalcMatch.Output.byPerson.

 CalcMatch --trueped true.ped --truedat true.dat --impped imp.ped --impdat imp.dat -o CalcMatch.Output --accuracyByGeno --byGeno --byPerson 

Will generate CalcMatch.Output.bySNP (6+20+6 fields only) and CalcMatch.Output.byPerson.