Reads a VCF/VCF.gz/BCF and removes all genotype information from it while retaining all site level information, including annotations based on genotypes (e.g. AN, AF). Output an be any support variant format including .vcf, .vcf.gz or .bcf.
java -jar picard.jar MakeSitesOnlyVcf
INPUT (File) Input VCF or BCF Required.
OUTPUT (File) Output VCF or BCF to emit without per-sample info. Required.
SAMPLE (String) Optionally one or more samples to retain when building the 'sites-only' VCF. Default value: null. This option may be specified 0 or more times.