Hi Plink users,
I am very new in GWAS and decided to use PLINK for this. But I am struggling with file formats.
I have one exome data with 200000 SNPs in it. But it is in .txt format. But all the necessary fields are there in different columns.
Can you please suggest me how I can create the plink .bed file?
Is there any direct way to create .bed file from .txt?
I tried to create a .bim and a .fam file following the instruction in PLINK website Binary files (BED/BIM/FAM)
Is there any way to create .bed file from these two (.bim & .fam) files?
Please let em know.
Thanks a lot,
Suparna.
Sample Name SNP Name Sample ID Allele1 - Top Allele2 - Top GC Score Allele1 - Forward Allele2 - Forward Allele1 - Design Allele2 - Design Allele1 - AB Allele2 - AB Allele1 - Plus Allele2 - Plus Chr Position GT Score Cluster Sep SNP ILMN Strand Customer Strand Top Genomic Sequence Plus/Minus Strand Theta R X Y X Raw Y Raw B Allele Freq Log R Ratio CNV Value CNV Confidence
200610-104 P001 A A 0.4097 T T T T A A T T MT 212 0.8207 1.0000 [T/C] BOT BOT + 0.010 2.315 2.281 0.034 35825 464 0.0042 -0.1955
200610-106 P001 A A 0.2638 T T A A A A A A MT 246 0.7865 1.0000 [A/G] TOP BOT + 0.106 2.202 1.884 0.318 29655 3030 0.0661 -0.3255
200610-119 P001 A A 0.3616 T T T T A A T T MT 5049 0.7771 1.0000 [T/C] BOT BOT + 0.035 2.515 2.382 0.133 37410 1369 0.0000 -0.0959
200610-137 P001 A A 0.3616 T T T T A A T T MT 12286 0.7771 1.0000 [T/C] BOT BOT + 0.086
Now obviously for Plink (Whole genome data analysis toolset....which is a comandline program for GWAS ) I don't need all the columns. So I managed to create bim and fam files using awk. But now I need binary bed file (which is not liek usual .bed files). That is why I was looking for any user who used PLINK before.
I think there are some option like --make-bed supplying bim and fam files; but I am not sure if I am doing it right.
Any help will be really great
Thanks a lot,
Mitra
Moderator's Comments:
edit by bakunin: Please use code tags next time for your code and data.
Hello Corona688,
Thanks for your reply. But I also have seen this. But this is Given test.ped and test.map, but I have only bim and fam and I want to create bed file. Given .ped and .map, program automatically create bim,bed,fam 3 files. But I want to go from bim and fam 20 bed file.
Thanks,
Mitra
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