SnpSift RmInfo

Remove INFO fields from a VCF file.

This is typically used before re-annotating a VCF file: since SnpEff and SnpSift add annotations without replacing existing ones, you should first remove old annotations and then re-annotate. This avoids ambiguity about whether a value comes from old or new annotations.

Usage

java -jar SnpSift.jar rmInfo [options] file.vcf infoField_1 [infoField_2 ... infoField_N] > output.vcf
Options:
    -id : Also remove the ID column (set to empty).

The first positional argument is the VCF file. All subsequent positional arguments are names of INFO fields to remove. Multiple fields can be removed in a single pass.

Info

The ##INFO header definitions for removed fields are NOT removed from the header. Only the actual values in data lines are stripped.

Example

Remove the EFF and ANN fields before re-annotating:

$ java -jar SnpSift.jar rmInfo input.vcf EFF ANN > input.clean.vcf

$ java -jar SnpSift.jar rmInfo input.vcf EFF
#CHROM  POS     ID      REF  ALT  QUAL  FILTER  INFO
1       734462  1032    G    A    .     s50     AC=348