From Illumina Final report to PLINK input

Question

[lisesandenbergh]

Received back the Final report (and accompanying files) for Illumina (ovine) SNP chip results and would now like to analyse the data in PLINK. In the past I used the PLINK plug-in for Genomestudio to create a .ped and .map files for PLINK. Unfortunately I no longer have access to Genomestudio, so I have been looking into using the .lgen format. I have been struggling to get the results from the Final report into the .lgen format using R. Is there a simpler way?

Answer 1

[njbernstein]

I had to do this recently (C: Recoding lgen into Ped using plink)

​awk 'NR > 11 { next }  !seen[$2]++ {print $2,$2,0,0}' final_report.txt > Plate3_final_report.fam
awk 'NR > 11 { next }  {print $2,$2,$1,$3,$4}' Plate3_final_report.txt > Plate3_final_report.lgen
awk 'NR < 2 { next } {print $3,$2,0,$4}' SNP_Map.txt > Plate3_final_report.map