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)
Source fles (FORTRAN) for calculations of SNP6 data (Birdseed-nr.txt)
poster 402, HGM2012, Sydney
Linkage and next generation sequencing (NGS) data in six large Danish families with dyslexia
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)
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 (renames)
Download Lip1234.EXE
input file: for001.dat
output file: for002.dat
Can only work on 16-32 bit PC
input for002.dat
Download udskrift.exe
output lipdata.dat
input lipdata.dat
extract-1.exe
exe files (can be maked by Fortran 99 using source the files
Download extrakt-1.exe
output SKE-snp6.txt
input fil to all: SKE-snp6.txt
Download extrakt-2alfa.exe
Download extrakt-3alfa.exe
Download extrakt-4alfa.exe
output files: chromosom-#.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
Download: figur-cm.exe
Download: figur-cm.txt (source file, renames to figur-cm.for)
Sortering of SKE-snp6.txt with Cygwin.exe
SKE-snp6.txt must be located in C:\Cygwin\home\'yourfolder'
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Hans Eiberg (unpublished)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