GAIN: Efficient genome ancestry inference in complex pedigrees with inbreeding[ Paper in ISMB 2010 ]
[ Download the software ]
Usage: GAIN.exe <FounderFile> <StrainFile> <FunnelFile> <#Generation> [options]
-cm: file containing genetic locations of SNP markers (in CM distance)
-bp: file containing physical locations of SNP markers
-s: m/f to indicate gender
-e: estimated error rate
-x: x chromosome
-of: output format (0/1)
either one of -cm or -bp must be used
( The program only models chromosome 1-19 accurately. The calculation on
X chromosome is a crude approximation. )
GAIN.exe Founders.txt Strain.txt Funnel.txt 11 -bp Bp_location.txt -e 0.01
All SNP values must be in 0,1,2,N (not A/T/C/G)
Founder File: The genotype sequence of the 8 founders are to be provided in 8 columns separated by comma:
No missing value is allowed in founder file. Only 0 and 1 can appear in founder file.
( since all founders are supposed to be fully inbred).
0: allele 1
1: allele 2
Strain Genotype File:
The genotype value of the strain to be analyzed can be in 0,1,2,N.
Each line consists of one value:
0: both allele 1
1: allele 1 + allele 2
2: both allele 2
Funnel Configuration File:
The file contains the funnel order of the 8 founders.
Genetic/Physical location file:
The file contains the Genetic/Physical locations of all SNP sites.
The result is stored in "<StrainFile>.prob".
Each line consists of segments in the pattern of: "(Founder X, Founder Y), probability"
Each line consists of 36 probability values. They represents the probability of founder pairs:
where ABCDEFGH are the 8 founders in the founder file.