Renaming and dropping annotations
in a DVCF

At a glance

In some cases, an annotation’s name (rather than value) changes between the Primary and Luft renditions. This happens in case of a REF⇆ALT switch for annotations with a name that contains a reference to the REF or ALT allele (for example: ALT_F1R2), and in case of a strand reversal where the annotation name contains a reference to the strand, for example ADF. In some other cases, the annotation makes no sense in the Luft coordinates, and should be dropped entirely. Genozip implements annotation dropping by adding a “DROP_” prefix to their name.

Genozip default annotation renaming and dropping

Annotations that are renamed by default:

Annotation	Type	Renamed to	Upon
MAX_AF	INFO	DROP_MAX_AF	REF⇆ALT switch
CLNHGVS	INFO	DROP_CLNHGVS	Always
ADF	FORMAT	ADR	Strand reversal
ADR	FORMAT	ADF	Strand reversal
RDF	FORMAT	RDR	Strand reversal
RDR	FORMAT	RDF	Strand reversal
F1R2	FORMAT	F2R1	Strand reversal
F2R1	FORMAT	F1R2	Strand reversal
REF_F1R2	FORMAT	REF_F2R1 ALT_F1R2 ALT_F2R1	Strand reversal REF⇆ALT switch REF⇆ALT + Strand
ALT_F1R2	FORMAT	ALT_F2R1 REF_F1R2 REF_F2R1	Strand reversal REF⇆ALT switch REF⇆ALT + Strand
REF_F2R1	FORMAT	REF_F1R2 ALT_F2R1 ALT_F1R2	Strand reversal REF⇆ALT switch REF⇆ALT + Strand
ALT_F2R1	FORMAT	ALT_F1R2 REF_F2R1 REF_F1R2	Strand reversal REF⇆ALT switch REF⇆ALT + Strand

The --dvcf-rename option

Annotations may be renamed by specifying the --dvcf-rename command line option, together with --chain, for example:

genozip myfile.vcf --chain mychain.chain.genozip --dvcf-rename=FORMAT/ADF:STRAND>ADR|REFALT>DROP_ADF

The argument is a comma-separated list of all annotations that need to be renamed (this example contains only one annotation - FORMAT/ADF):

- The annotation name (FORMAT/ADF in this case) can be the name only (eg ADF), or prefixed with INFO/ or FORMAT/ to resolve ambiguity.

- The rules for renaming the particular annotation are specified as a | (pipe)-separated list to the right of the colon. In the example above, we have two rules: STRAND>ADR and REFALT>DROP_ADF.

- Each rule consists of an event and a destination annotation name, separated by a > (greater-than) character. The event can be one of the four:

Rule	Rule activated upon
STRAND	Strand reversal
REFALT	REF⇆ALT switch
TLAFER	Concurrent strand reversal and REF⇆ALT switch
ALWAYS	Always

The --dvcf-drop option

Annotations may be dropped with the --dvcf-drop command line option, for example:

genozip myfile.vcf --chain mychain.chain.genozip --dvcf-drop=INFO/MAX_AF:REFALT

This is equivalent of --dvcf-rename=INFO/MAX_AF:REFALT>DROP_MAX_AF

To override Genozip’s default renaming, just rename the tag to itself, for example:

--dvcf-rename=INFO/MAX_AF:ALWAYS>MAX_AF

The --show-rename-tags option

--show-rename-tags can be used in combination with --chain or when compressing a DVCF file, to display the list of annotations that are to be renamed.