I have a file like this: (has 308545 lines)
head output11.frq
CHR SNP A1 A2 MAF NCHROBS
1 1:775852:T:C T C 0.1707 3444
1 1:1120590:A:C C A 0.08753 3496
1 1:1145994:T:C C T 0.1765 3496
1 1:1148494:A:G A G 0.1059 3464
1 1:1201155:C:T T C 0.07923 3496
...
And another file (marker-info) which has the first 24 commented lines
and is comma separated that looks like this (has total of 500593
lines):
1,742429,SNP_A-1909444,ss66079302,rs3094315,36.2,G,A,C,T,A,GCACAGCAAGAGAAAC[A/G]TTTGACAGAGAATACA,Sty,+,-,y,,,127,phs000018
1,769185,SNP_A-4303947,ss66273559,rs4040617,36.2,A,G,A,G,A,GCTGTGAGAGAGAACA[A/G]TGTCCCAATTTTGCCC,Sty,+,+,n,,,127,phs000018
1,775852,SNP_A-1886933,ss66317030,rs2980300,36.2,T,C,A,G,A,GAATGACTGTGTCTCT[C/T]TGAGTTAGTGAAGTCA,Nsp,-,+,y,,,127,phs000018
1,782343,SNP_A-2236359,ss66185183,rs2905036,36.2,C,T,C,T,A,CTCGATTTGTGTTCAA[C/T]ATATTTCATTTGTACC,Sty,-,-,n,,,127,phs000018
1,1201155,SNP_A-2205441,ss66174584,rs4245756,36.2,C,T,C,T,A,CCAGTGCTTTCAACCA[C/T]ACTCACTTTTCACTGT,Sty,+,+,n,,,127,phs000018
...
I want to replace in output11.frq second column with the 5th column in
marker-info that has the matching value in 1st and 2nd column so for
this example the result of the output11.frq would look like this:
1 rs2980300 T C 0.1707 3444
1 rs4245756 T C 0.07923 3496
I tried doing this in bash but I got empty file:
vi tst.awk
NR==FNR { map[$1,$2]=$5; next }
($1,$4) in map { $2=map[$1,$4]; print }
awk -f tst.awk FS=',' marker-info FS='\t' output11.frq > output11X.frq
Can this be done in R?
Thanks
Ana
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