Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file.
java -jar picard.jar CollectVariantCallingMetrics
INPUT (File) Input vcf file for analysis Required.
OUTPUT (File) Path (except for the file extension) of output metrics files to write. Required.
DBSNP (File) Reference dbSNP file in dbSNP or VCF format. Required.
TARGET_INTERVALS (File) Target intervals to restrict analysis to. Default value: null.
SEQUENCE_DICTIONARY (File) If present, speeds loading of dbSNP file, will look for dictionary in vcf if not present here. Default value: null.
GVCF_INPUT (Boolean) Set to true if running on a single-sample gvcf. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
THREAD_COUNT (Integer) Default value: 1. This option can be set to 'null' to clear the default value.