Converts VCF to BCF or BCF to VCF. This tool converts files between the plain-text VCF format and its binary compressed equivalent, BCF. Input and output formats are determined by file extensions specified in the file names. For best results, it is recommended to ensure that an index file is present and set the REQUIRE_INDEX option to true.
java -jar picard.jar VcfFormatConverter I=input.vcf O=output.bcf REQUIRE_INDEX=true
INPUT (File) The BCF or VCF input file. Required.
OUTPUT (File) The BCF or VCF output file name. Required.
REQUIRE_INDEX (Boolean) Fail if an index is not available for the input VCF/BCF Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}