I have two text files:
file 1:
#CHROM POS ID REF ALT
1 61442 rs2531261 A G
1 924629 rs28622096 A G,T
1 974662 rs2465135 G T
1 995481 rs9442393 T G
file 2
#CHROM POS ID REF ALT FORMAT
1 61442 rs2531261 A G GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1 924629 rs28622096 A G,T GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1 974662 rs2465135 G T GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1 987909 rs34235844 G GTG GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1 995481 rs9442393 T G GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
I would like to combine the files based on column 3 (ID). My output file should like:
output:
#CHROM POS ID REF ALT FORMAT
1 61442 rs2531261 A G GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1 924629 rs28622096 A G,T GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1 974662 rs2465135 G T GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1 995481 rs9442393 T G GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
I want to use awk
.
file 1
that is not already infile 2
? It's not clear from your question.