make ped file from SNPChip final_report

Question

[mary]

Hi All

I have a file which Here are the first 14 lines of an Illumina "Final Report" CSV file:

[Header]
GSGT Version    1.9.4
Processing Date 6/16/2015 3:09 PM
Content         SheepHD_AgResearch_Cons_15041608_A.bpm
Num SNPs        606006
Total SNPs      606006
Num Samples     43
Total Samples   228

[Data]
SNP Name        Sample Name     Allele1 - Top   Allele2 - Top   GC Score
250506CS3900140500001_312.1     Black   A       G       0.9562
250506CS3900176800001_906.1     Black   G       G       0.9347
250506CS3900211600001_1041.1    Black   C       C       0.7965
250506CS3900218700001_1294.1    Black   A       A       0.8392

I search to make ped and mp file and find " https://groups.google.com/forum/#!topic/plink2-users/LgdRh9mjlGc"

I used

tail -n+11 FinalReport.csv | cut -d, -f3,4 | tr -d ',' | tr -- '-\n' '0 ' | perl -pe 's/((([^ ]{2} ){1542}){1543}([^ ]{2} ){549})/$1\n/g' > test.out

its work but when I do

wc -l test.out

I get 10 sample instead of 43 sample (at head of final report write the file have 43 sample). I dont know where I made mistak.

dose anybody have any suggestion?

tnx

[NB]

Read here and here