how to extract cleaned SNPs from the main genotype data after QC?

Question

[taghizadehkobra]

Hi there I have a genotype data file with 54242 SNPs. With quality control, 43,456 SNPs remained. Now I want to extract just cleaned SNPs (43,456 SNPs) from the genotype data.

Thanks in advance

[evolozzy]

Can you clarify your question?

1. What is the file format? GEN, VCF, BED etc are all genotype data files.
2. What exactly do you need? The positions of SNPs or something else.

[taghizadehkobra]

Thank you for replying! Below is a part of my data file! The "Name1" column is SNP names and has 52242 rows.

** Name1    Log R Ratio B Allele Freq
 250506CS3900065000002_1238.1   0.0272  0.9957
 250506CS3900140500001_312.1    0.1311  0.9896
 250506CS3900176800001_906.1    -0.1012 1
250506CS3900211600001_1041.1    0.0212  0.999**

After performing quality control on all 54242 SNPs with Plink softwar, 47256 SNPs passed from QC as follow!

Name2
250506CS3901300500001_1084.1
CL635241_413.1
CL635750_128.1
CL635944_160.1
Contig35697_5761.1
CytB_1505.1
CZ923139_448.1

Now I want to replace the column (Name2) with column (Name1)!in fact I need to have just 47256 SNPs passed among all 54242 total SNPs! I hope my explanation is clear!

[Pierre Lindenbaum]

same answer as : A: how to combine two bed files using the same ID information