| findhap.f90 |
Find haplotypes and impute genotypes using multiple
chip sets. |
| DOWNLOAD: |
Version 2 program, example
files, and executable |
| INPUTS: |
|
|
genotypes.txt |
Format: animal# chip# #SNPs genotypes
Sort by
animal#, genotype codes are 0,1,2, and 5 = missing
For fixed length input,
set chip# to 1 and missing genotypes to 5
For variable length input, #SNPs
and order must match chromosome.data |
|
chromosome.data |
List of all SNPs used and which SNPs are on each chip
Sort by
chromosome number and position within chromosome
X-specific chromosome last,
after pseudo-autosomal 'chromosome'
Y-specific SNP not supported yet |
|
pedigree.file |
Format:
sex animal# sire# dam# birthdate animal
ID animal name
Sort in ascending birth date order |
|
findhap.options |
Program control file with user-defined options |
| OUTPUTS: |
|
|
hap.list |
List of all haplotypes found in each segment |
|
hap.found |
Each animal's paternal and maternal haplotypes (2 lines / animal)
|
|
hap.inherit |
Tracks inheritance and crossovers for each parental chromosome
|
|
hap.filled |
Summarize imputation quality for each animal |
|
cross.overs |
Lists exact location of all detected crossovers |
|
allele.frequency |
Estimated allele frequencies and missing rates for each SNP |
|
genotypes.filled |
Imputed genotypes with codes: 0 = BB, 1 = AB, 2 = AA, 3 = B_, 4 =
A_, 5 = __
Number of animals output may exceed input because of imputed
dams
Remaining missing alleles in code 3, 4, and 5 can be set using allele
frequencies |
|
haplotypes.txt |
Imputed haplotypes: SNP1 paternal maternal, SNP2 pat mat, etc for
each animal
No missing alleles, allowing genotypes to be formed simply as
(pat + mat - 2) |
|
|
| VERSION 1 REFERENCES: |
2010
Interbull Bulletin 42, 4
pages
2010 9th World
Congress Genetics Appl. Livest. Prod., Comm. #27
2011
Genetic
Selection Evolution (submitted) |
| VERSION 2 DIFFERENCES: |
Options file uses maxlen, minlen, and steps to divide
long segment into shorter segments.
Computing time increases by number of
steps used to get from maxlen to minlen.
Population and pedigree
haplotyping in one loop vs. 2 separate loops.
Searches for great
grandparent haplotypes, not just genotyped parents and grandparents.
Higher
accuracy and / or fewer high density genotypes required. |
| LICENSE: |
Fortran program findhap.f90 is public domain and was
developed with US taxpayer funding. Accurate results are not guaranteed. Please
report any bugs to Paul.VanRaden@ars.usda.gov. You
may modify, improve, use, and redistribute the code to anyone for any purpose.
Or, you can ask Paul to make changes that could benefit US evaluations and
other users. |