SNP6-LINK

Linkage program for calculations of mil. of 2-point Lod scores. This program package
make input files for LIPED (slightly modified to LIP1234 so it can read chrom. and Bp positions of SNP's)
After calculations the lod scores the program can extract data to Exel files. Windows XP/ 7 (32 bit), Lotus

Source fles (FORTRAN) for calculations of SNP6 data (Birdseed-nr.txt)
poster 402, HGM2012, Sydney

Input file for LIP1234 (LIPED)
hoved-rec.txt (recessive inheritance)
hoved-dom.txt (dominant inheritance)
hoved-dom-p.txt (dominant inheritance with penetrance)
hoved-xrec.txt (X-recessive inheritance)
hoved-xdom.txt (X-dominante inheritance)
split1.txt (Family structure with 19 lines)
split1.txt (Family structure with 38 lines)
for001.dat (Family structure with 38 lines, chromosome and possision 3 910987654 from Birdseed files)
for002.dat output file for Udskrift.exe- with chromosome and possision 3 910987654 from Birdseed files)

Procedure
input file: combinated Birdseed files in one file by use of EXEL: geno-types.txt
Tabulator separated (tab):
comb-38-30-dom.txt (renames to .for and compiles with Fortran 99)
Use split1.txt with 38 lines and extract data from 30 birdseed genotypes, chromosome and Base pair prompt g77 comb-38-30-dom.for
out a.exe (run this file to make an input file: for001.dat to Lip1234.exe)

Lip1234.exe (modified LIPED reading SNP's locations (source file below) Can only work on 16-32 bit PC
output file: for002.dat

input for002.dat
udskrift.exe (source file below)
output lipdata.dat

input lipdata.dat to
extract-1.exe
output SKE-snp6.txt
input SKE-snp6.txt
extrakt-2alfa.exe
extrakt-3alfa.exe
extrakt-4alfa.exe
exe files (can be maked by Fortran 99 /77 using source the files below, renames txt to xxx.for
output chromosome#.txt

Source files
all txt-files must be renamed from .txt to .for and combilated with a FORTRAN 99 compiler
Download: extrakt-1.txt
Download: extrakt-2alfa.txt
Download: extrakt-3alfa.txt
Download: extrakt-4alfa.txt
Download: udskrift.txt
Download: LIPED source file, for Fortran 77 compiler


Sorting data to chromosome plot: Cygwin (or can be done in EXEL word)
$ cat.exe SKE-snp6.txt |sort.exe | uniq.exe -c >resultat.txt
figur-cm.exe program
Download: figur-cm.txt (source file, renames to figur-cm.for)

Sortering of SKE-snp6.txt with Cygwin.exe or EXEL

Reference:
Hans Eiberg (unpublished)
P204 HGM2012
Fast Linkage calculation of Affymetrix SNP 6.0 genotype data using a new program SNP6-LINK
Hans Eiberg and Lars Hansen