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From Illumina Final report to PLINK input
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?
snp genome
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updated by njbernstein • njbernstein • written by lisesandenbergh • lisesandenbergh

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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
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updated by Ram Ram • written by njbernstein • njbernstein

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