Famhap
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FAMHAP
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General description
FAMHAP is a software for the haplotype analysis of unphased genotype data of tightly linked markers. It can be used both for the analysis of case-control data and the analysis of nuclear family data (parents with an arbitrary number of children). The program is optimized for the haplotype frequency estimation of many markers. A theoretically possible number of 263 haplotypes is allowed.
Application homepage
http://www.uni-bonn.de/~umt70e/becker.html
Proper citation
Becker T, Knapp M. Maximum-likelihood estimation of haplotype frequencies in nuclear families. Genet Epidemiol 2004; 27: 21-32.
Quick start
To start running FAMHAP you only need one input file - see below.
Input file format
FAMHAP uses a simplified linkage format:
FID PID MO FA SEX AFF M1_A M1_B M2_A M2_B ....
Useful commands
The basic command line is: famhap "infilename" "outfilename" "options" (the three first parameters are filled in automatically)
The "options" are
- "#" "#" ..: select markers (e.g. 1 4 5, estimate only for markers 1, 4 and 5)
- u: missing genotypes included (at least one genotype must be available in a family)
- u1, u60, u70, u80, u90, u95, u99, u100: include individuals with acceptable missing rate as well (# is % markers genotyped, except u1 where at least one genotype per family must be available)
- it: compute haplotype frequencies in locus-iterative mode (obligatory for analysis of >20 SNPs)
- itt: progressive extension technique in two directions plus estimation with inferred parameter set
- dp: estimation with respect to affection status
- P: enhanced output (all haplotype frequencies different from zero are printed instead of default >1%)
- PP: even more enhanced output..
- ed: systematic search for potential genotyping errors
Please note that the option "quiet" should be added by default.
Example:
famhap16 test.txt testout.txt 1 4 5 u60 it dp P ed
Output files
- "outfilename": haploytpe frequencies
- "outfilename"_LDmeasures: LD measures, for import into GOLD program by Abecasis (http://www.sph.umich.edu/csg/abecasis/GOLD/)
- "outfilename".gm: genetic map, needed for GOLD import
- "outfilename"_H1_HAPLOTYPES: most likely haplotype explanation (in each family)
- "outfilename"_MENDELERRORS: any Mendelian errors