When I convert a VCF file to Plink (PED and MAP files), using
$ vcftools --gzvcf myfile.vcf.gz --plink --out myfile_plink
there are too few variants in the PED file. The MAP file has the correct amount of variants (same as in original VCF file), but the PED file has much fewer. If I try to run some Plink command on these files, Plink reports this inconsistency, and I can verify it as well.
Working with a file with just chromosome 1 (human genome) seems to work just fine, but when combining all chromosomes (
vcf-concat) I get this problem.
When processing on a per-chromosome basis, this happens sometimes as well.