#!/bin/bash -euo pipefail
plink2 \
    --threads 10 \
    --memory 20480 \
    --set-all-var-ids '@:#:$r:$a' \
    --max-alleles 2 \
    --new-id-max-allele-len 100 missing \
    --vcf NG1RDRPK1V.vcf.gz  \
    --make-pgen vzs\
    --out vcf_NG1RDRPK1V_ALL # 'vcf_' prefix is important

cat <<-END_VERSIONS > versions.yml
"PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF":
    plink2: $(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*$//' )
END_VERSIONS
