Lifts over a VCF file from one reference build to another. This tool adjusts the coordinates of variants within a VCF file to match a new reference. The output file will be sorted and indexed using the target reference build. To be clear, REFERENCE_SEQUENCE should be the target reference build. The tool is based on the UCSC liftOver tool (see: http://genome.ucsc.edu/cgi-bin/hgLiftOver) and uses a UCSC chain file to guide its operation. Note that records may be rejected because they cannot be lifted over or because of sequence incompatibilities between the source and target reference genomes. Rejected records will be emitted with filters to the REJECT file, using the source genome coordinates.
java -jar picard.jar LiftoverVcf I=input.vcfO=lifted_over.vcfCHAIN=b37tohg19.chainREJECT=rejected_variants.vcfR=reference_sequence.fasta
INPUT (File) The input VCF/BCF file to be lifted over. Required.
OUTPUT (File) The output location to write the lifted over VCF/BCF to. Required.
CHAIN (File) The liftover chain file. See https://genome.ucsc.edu/goldenPath/help/chain.html for a description of chain files. See http://hgdownload.soe.ucsc.edu/downloads.html#terms for where to download chain files. Required.
REJECT (File) File to which to write rejected records. Required.
REFERENCE_SEQUENCE (File) The reference sequence (fasta) for the TARGET genome build. The fasta file must have an accompanying sequence dictionary (.dict file). Required.
WARN_ON_MISSING_CONTIG (Boolean) Warn on missing contig. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
WRITE_ORIGINAL_POSITION (Boolean) Write the original contig/position for lifted variants to the INFO field. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
LIFTOVER_MIN_MATCH (Double) The minimum percent match required for a variant to be lifted. Default value: 1.0. This option can be set to 'null' to clear the default value.
ALLOW_MISSING_FIELDS_IN_HEADER (Boolean) Allow INFO and FORMAT in the records that are not found in the header Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}