When filtering SNP, how can I preserve all information in the FORMAT column?

[qimin1125]

When using the command plink2 --vcf file.vcf --maf 0.05 --geno 0.05 --hwe 0.0001 --recode vcf-iid --out output --allow-extra-chr --max-alleles 2 --double-id to filter a VCF file, the resulting output.vcf file only retains the GT information in the FORMAT column. How can I preserve other information, such as AD, DP, etc., in the FORMAT column as well?

[NorthblueM]

You might be looking for a different tool with the same name, PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

The pLink described in this repository is a search engine designed for identifying cross-linked protein complexes or proteomes from mass spectrometry data.