Edit Column sex in ped file

Question

[mm]

I want to edit my column sex in ped file and place in numbers 2 and 1 instead of F and M . How do I do this Linux?

[mm]

Despite Individual ID Paternal ID Maternal ID- how to build Family ID?

[WouterDeCoster]

How to build a family ID?

[mm]

           yes

Answer 1

[Pierre Lindenbaum]

awk '{OFS="\t";if($5=="M") {$5="1";} else if($5=="F") {$5="2";} else {$5="0";}print;}' in.ped > out.ped

[mm]

The output file as follows: It seems that is wrong

SNP Chip    ID  Animal  0   Paternal
R950E03 111006  930226  910008  0   Resistant
R950E06 110917  950085  910043  0   Resistant
R950C09 110892  950085  910125  0   Resistant
R949B05 111101  870141  840409  0   Resistant

[Pierre Lindenbaum]

I assumed that the sex is in column $5 and there is no header:

$ echo "FAM ID FATHER MOTHER M" | awk '{OFS="\t";if($5=="M") {$5="1";} else if($5=="F") {$5="2";} else {$5="0";}print;}'
FAM ID  FATHER  MOTHER  1

[WouterDeCoster]

From: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory:

 Family ID
 Individual ID
 Paternal ID
 Maternal ID
 Sex (1=male; 2=female; other=unknown)
 Phenotype