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Binary Bim File To Agct Bim Format

Hi All,

I have a SNP data genotyped with Affymatrix 6.0 Chip. Its BIM file is in 1234 format. e.g.

1    rs3094315    0    792429    3    1
1    rs11240776    0    805132    3    1
1    rs2980319    0    816985    1    4
1    rs2905036    0    832343    2    4

And I want to convert it in to AGCT format. e.g.

1    rs3094315    0    792429    C    A
1    rs11240776    0    805132    C    A
1    rs2980319    0    816985    A    T
1    rs2905036    0    832343    G    T

thanks

snp affymetrix
• 3,210 views • link
updated by Biostar Biostar • written by User 0422 • User 0422

2 answers

If your using PLINK, try --alleleACGT.

• 4 views • link
written by Maxime Lamontagne Maxime Lamontagne

You could combine the unix commands tr and cut

while read L
do
   echo $L | cut -d '  ' -f 1,4 | tr -d "\n"
   echo -n  " "
   echo  $L | cut -d ' ' -f 5 | tr "1234" "AGCT" | tr -d "\n"
   echo -n " "
   echo $L | cut -d ' ' -f 6 | tr "1234" "AGCT" 
done  < yourfile.txt | tr " " "\t"
• 2 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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