setwd("/net/ifs1/san_projekte/projekte/genstat/09_nutzer/roshyara/programs/eigensoft/EIG5.0.1/CONVERTF/")
getwd()
## [1] "/net/ifs1/san_projekte/projekte/genstat/09_nutzer/roshyara/programs/eigensoft/EIG5.0.1/CONVERTF"
Read ped and map file:
echo "plink ped file"
cat fcgene_out.ped
echo "plink map file:"
cat fcgene_out.map
echo "Now I use the follwoing script to convert into eigenstrat "
echo "-------------------------------------------"
cat par.fcgene.eigenstart
echo "-------------------------------------------"
echo "running convertf"
echo "-------------------------------------------"
../bin/convertf -p par.fcgene.eigenstart
echo "This command has created the following three files. and there is nothing change. Its similar to
map file"
echo "-------------------------------------------"
echo "snp file"
cat fcgene_out.snp
echo "-------------------------------------------"
echo indfile
cat fcgene_out.ind
echo "-------------------------------------------"
echo eigenstratfile
cat fcgene_out.eigenstratgeno
echo "-------------------------------------------"
## plink ped file
## KGA-B-B1-Ls081 KGA-B-B1-Ls081 0 0 1 1 T G T T G G C T T T G A A A C T G A G C C C G A G G G A A A G G A C C C A G G G A G C C C C C C C C G G C C C C A A C C
## KGA-S-B1-Ls067 KGA-S-B1-Ls067 0 0 1 1 G G T T G G C C T T G A A G C T G A G C C C G A G G G A A A G G A C C C G G G G A G C C C C C C C T G G C C C C A A C C
## LRS-B-B1-Ls038 LRS-B-B1-Ls038 0 0 1 2 T G T T G G C T T T G G A A T T A A G C C C A A G G G A A A G G A C C A A G G G G G C C C C G G C C G G C T C C A A C C
## LRS-B-B1-Ls043 LRS-B-B1-Ls043 0 0 2 2 G G T T G G C T T T A A A A C T G A C C C C A A G G G A A A G G A C C C A G G G A G C C C C C C C C G G C C C C A A C C
## LRS-B-B1-Ls063 LRS-B-B1-Ls063 0 0 1 1 T G T T G C T T T T A A A A T T G G G G C C A A G G G A A A G G C C C A A G G G G G C C C C C G C C G G C C C C A A C T
## LRS-B-B1-Ls064 LRS-B-B1-Ls064 0 0 1 2 T G T T G G T T T T G A A A T T G G G C C C G A G G A A A A G G A A C A A G G G G G C T C C G G C C G G C C C C A A C C
## LRS-B-B1-Ls114 LRS-B-B1-Ls114 0 0 2 1 T T T T G C T T T T G A G G T T G A G G C C G A G G A A A A G G C C C C A A G G G G C C C C C G C C G G C C C C A A C C
## LRS-B-B1-Ls117 LRS-B-B1-Ls117 0 0 2 2 T T T T G C T T T T G A A G C T G A G G C C G A G G G A A A G G A C C A A A G G G G C T C C G G C C G G C C C C A A C C
## LRS-Q-B2-W_I07 LRS-Q-B2-W_I07 0 0 1 1 T G T T G G T T T T A A A A T T G G C C C C A A G G G A A A G G A C C A A G G G G G C C C C C C C C G G C C C C A A C C
## LRS-Q-B3-W_K06 LRS-Q-B3-W_K06 0 0 2 2 G G T T G C C T T T G A A A T T G A C C C C G A G G A A A A G G A C C C A A G G G G C T C C C G C C G G C C C C A A C C
## LRS-Q-B3-W_O06 LRS-Q-B3-W_O06 0 0 1 2 G G T T G C T T T T A A A A T T G A C C C C G A G G G A A A G G A C C A G G G G G G C T C C G G C C G G C C C C A A C C
## LRS-Q-B3-W_O07 LRS-Q-B3-W_O07 0 0 2 1 T G T T G G T T T T G A A A T T G A G C C C G A G G G G A A G G A C C A A G G G A G C T C C C G C T G G C C C C A A C C
## LRS-Q-B3-W_S06 LRS-Q-B3-W_S06 0 0 1 2 T G T T G G T T T T G A A G C T A A C C C C G G G G A A A A G G A C C A G G G G A G C T C C C G C C G G C C C C A A C T
## LRS-S-B3-W_CC02 LRS-S-B3-W_CC02 0 0 2 2 T G T T G G T T T T G A A A C C A A G C C C A A G G A A A A G G A A C A G G G G A G C C C C C G C C G G C C C C A A C T
## LRS-S-B3-W_CC07 LRS-S-B3-W_CC07 0 0 1 2 T G T T G G T T T T A A A G T T A A G C C C G A G G A A A A G G A C C A A G G G G G C C C C C G C C G G C C C C A A C C
## LRS-S-B3-W_CC10 LRS-S-B3-W_CC10 0 0 2 2 T G T T G G T T T T A A A G C T G A C C C C A A G G G G A A G G A A C C A G G G A G C C C C C G C C G G C C C C A A C C
## LRS-S-B3-W_CC11 LRS-S-B3-W_CC11 0 0 1 1 T G T T G C T T T T A A A A T T G A C C C C A A G G A A A A G G C C C A A G G G A G C T C C C G C C G G C C C C A A C T
## LRS-S-B3-W_FF30 LRS-S-B3-W_FF30 0 0 1 2 T G T T G G T T T T G G A G T T G G G C C C A A G G G A A A G G A C C C A A G G G G C T C C G G C C G G C C C C A A C C
## LRS-S-B3-W_Y11 LRS-S-B3-W_Y11 0 0 1 1 G G T T G G C T T T A A A A T T G A C C C T A A G G A A A A G G A C C A A G G G A G C C C C C G C C G G C C C C A A C C
## LRS-S-B3-W_Z04 LRS-S-B3-W_Z04 0 0 2 1 T G T T G G C T T T G A A A T T A A G C C C A A G G A A A A G G C C C A A G G G G G C T C C C G C C G G C C C C A A C C
## plink map file:
## 22 rs7288834 0 16212142
## 22 rs16978746 0 20278224
## 22 rs5754387 0 20304703
## 22 rs5751603 0 21855082
## 22 rs8142454 0 24186116
## 22 rs614580 0 24236898
## 22 rs3859875 0 24540850
## 22 rs742942 0 26235428
## 22 rs2347790 0 27744001
## 22 rs2857648 0 28396568
## 22 rs1001318 0 28462167
## 22 rs8141732 0 30848102
## 22 rs7364159 0 31383786
## 22 rs3819662 0 32295497
## 22 rs5994821 0 32737803
## 22 rs134415 0 33913297
## 22 rs5756090 0 34915555
## 22 rs130437 0 35699411
## 22 rs229541 0 35921264
## 22 rs2267368 0 36895155
## 22 rs11704319 0 38052832
## 22 rs734561 0.52 42655437
## 22 rs5765756 0.55 43305340
## 22 rs5766295 0.57 43791963
## 22 rs17652822 0.6 44539893
## 22 rs17821852 0.62 45529058
## 22 rs136100 0.63 45739908
## 22 rs6009076 0.63 45741920
## 22 rs5767067 0.66 46999448
## 22 rs9628063 0.68 47746428
## Now I use the follwoing script to convert into eigenstrat
## -------------------------------------------
## genotypename: fcgene_out.ped
## snpname: fcgene_out.map # or example.map, either works
## indivname: fcgene_out.ped # or example.ped, either works
## outputformat: EIGENSTRAT
## genotypeoutname: fcgene_out.eigenstratgeno
## snpoutname: fcgene_out.snp
## indivoutname: fcgene_out.ind
## familynames: NO
## -------------------------------------------
## running convertf
## -------------------------------------------
## parameter file: par.fcgene.eigenstart
## genotypename: fcgene_out.ped
## snpname: fcgene_out.map
## indivname: fcgene_out.ped
## outputformat: EIGENSTRAT
## genotypeoutname: fcgene_out.eigenstratgeno
## snpoutname: fcgene_out.snp
## indivoutname: fcgene_out.ind
## familynames: NO
## genotype file processed
## numvalidind: 20 maxmiss: 20001
## eigenstrat output
## ##end of convertf run
## This command has created the following three files. and there is nothing change. Its similar to
## map file
## -------------------------------------------
## snp file
## rs7288834 22 0 16212142 G T
## rs16978746 22 0 20278224 T X
## rs5754387 22 0 20304703 G C
## rs5751603 22 0 21855082 T C
## rs8142454 22 0 24186116 T X
## rs614580 22 0 24236898 A G
## rs3859875 22 0 24540850 A G
## rs742942 22 0 26235428 T C
## rs2347790 22 0 27744001 A G
## rs2857648 22 0 28396568 C G
## rs1001318 22 0 28462167 C T
## rs8141732 22 0 30848102 A G
## rs7364159 22 0 31383786 G X
## rs3819662 22 0 32295497 A G
## rs5994821 22 0 32737803 A X
## rs134415 22 0 33913297 G X
## rs5756090 22 0 34915555 C A
## rs130437 22 0 35699411 C A
## rs229541 22 0 35921264 A G
## rs2267368 22 0 36895155 G X
## rs11704319 22 0 38052832 G A
## rs734561 22 0.520000 42655437 C T
## rs5765756 22 0.550000 43305340 C X
## rs5766295 22 0.570000 43791963 G C
## rs17652822 22 0.600000 44539893 C T
## rs17821852 22 0.620000 45529058 G X
## rs136100 22 0.630000 45739908 C T
## rs6009076 22 0.630000 45741920 C X
## rs5767067 22 0.660000 46999448 A X
## rs9628063 22 0.680000 47746428 C T
## -------------------------------------------
## indfile
## KGA-B-B1-Ls081 M Control
## KGA-S-B1-Ls067 M Control
## LRS-B-B1-Ls038 M Case
## LRS-B-B1-Ls043 F Case
## LRS-B-B1-Ls063 M Control
## LRS-B-B1-Ls064 M Case
## LRS-B-B1-Ls114 F Control
## LRS-B-B1-Ls117 F Case
## LRS-Q-B2-W_I07 M Control
## LRS-Q-B3-W_K06 F Case
## LRS-Q-B3-W_O06 M Case
## LRS-Q-B3-W_O07 F Control
## LRS-Q-B3-W_S06 M Case
## LRS-S-B3-W_CC02 F Case
## LRS-S-B3-W_CC07 M Case
## LRS-S-B3-W_CC10 F Case
## LRS-S-B3-W_CC11 M Control
## LRS-S-B3-W_FF30 M Case
## LRS-S-B3-W_Y11 M Control
## LRS-S-B3-W_Z04 F Control
## -------------------------------------------
## eigenstratfile
## 12121100122111111121
## 22222222222222222222
## 22221211211222221222
## 10112222212222222211
## 22222222222222222222
## 11022111212111222021
## 21222201222212112122
## 11212221222210212222
## 11210011011122211012
## 11120100222121122121
## 22222222222222222212
## 11222111211102122222
## 22222222222222222222
## 11111221121022202122
## 22222222222222222222
## 22222222222222222222
## 11112021111110102112
## 22121121121111121211
## 10111122120100111211
## 22222222222222222222
## 11212222222111211212
## 22222121211112221121
## 22222222222222222222
## 00201212012111111211
## 21222222222122222222
## 22222222222222222222
## 22122222222222222222
## 22222222222222222222
## 22222222222222222222
## 22221222222211221222
## -------------------------------------------