Allele frequncies in plink including physical position in the output

Question

[Famf]

Hi, I am trying to compute allele frequencies for a large genotypic data set. The command I am using is as follow:

plink2 --vcf my_file.vcf.gz --freq --map my_file.map --out my_outfile

The reason I am using a map file is because I want to include physical position of each marker in my output file.

The error is this:

Error: --vcf conflicts with another input flag 

[chrchang523]

Please explain exactly what you mean by "physical position", and why the VCF file doesn't have it. 'POS' is supposed to be a required VCF field.

[Famf]

My VCF files have physical position! The function --freq of PLINK2 yields allele frequencies but it does not include positions in output file. What do not have my VCF files is ID information. So, without ID and POS there is no way to use that frequencies in further analysis.

Answer 1

[chrchang523]

Many PLINK2 commands, including --freq, include a "column set descriptor" which can be used to customize which output columns appear.

General documentation on PLINK2 column set descriptors: https://www.cog-genomics.org/plink/2.0/general_usage#colset

List of column-sets supported by --freq: https://www.cog-genomics.org/plink/2.0/formats#afreq

[Famf]

Thanks for your reply. Yes, actually I read that information (in that link)before posting in this forum but I didn't find the way to add POS in the output of --freq. In that link it says --freq produces an output with the following columns: CHROM, ID, REF, ALT, ALT_FREQS, and OBS_CT. But not POS. Is there any option I need to add to my command to add POS to my output file?

[chrchang523]

Please reread both links.