Plink 2 has a general set of tools for outputting GWAS data into a tabular format. These may be more suitable for exploration and analyses in non-genomic specific platforms like R.
Here is an example where we export the variants in tabular form, with major axis (rows) as sample IDs.
Plink 2:
time plink2 \
--pfile 'vzs' ./data/raw/all_hg38 \
--export A \
--thin-count 10 --seed 111 --threads 1 --memory 8000 require \
--out ./data/export/all_hg38_thin10_exportA
--export A
The command call for exporting into a tabular form. Data is written with counts per variant to a human readable file *.raw file. Using the flag A allele dosage is written with samples as rows (sample-major) and column-wise haploid genotype dosages on a 0-2 scale. By default, REF alleles are counted (this is a change from PLINK 1.x); this can be adjusted with --export-allele. --export-allele's input file should have variant IDs in the first column and allele IDs in the second. If you need the ALT alleles to be named in the header line, add the 'include-alt' modifier.
Variations of this command include Av and AD flags. Av results in variant IDs as rows (variant-major). Unlike A exported sample-major files, Av files can be imported back into Plink 2 using --import_dosage. AD results in both additive counts and a heterozygous boolean field (0/1) for dominance-deviation models.
See --export for more information on these commands.