index.md

VcfAnnotateFromVcf documentation

Single annotation source file

When annotating from a single source VCF file, you can do that using command line parameters only.

If the annotation source file source.vcf.gz contains the INFO keys A, B and C. You can annotate them to the input using:

    > VcfAnnotateFromVcf -in [input].vcf[.gz] -source source.vcf.gz -threads [threads] -info_ids A,B,C -out [output].vcf

If you want to annotate A, but want to rename the key to D, use this command:

    > VcfAnnotateFromVcf -in [input].vcf[.gz] -source source.vcf.gz -threads [threads] -info_ids A=D -out [output].vcf

If you want to annotate A, B and C and the ID column, use this command:

    > VcfAnnotateFromVcf -in [input].vcf[.gz] -source source.vcf.gz -threads [threads] -info_ids A,B,C -id_column ID -out [output].vcf

Multiple annotation source files

If you want to annotate information from several source VCF files, you can provide a config file:

    > VcfAnnotateFromVcf -in [input].vcf[.gz] -config_file [config_file] -threads [threads] -out [output].vcf

The config file is a tab-separated file that contains one line for each annoatation source file.
The following columns are required in each line:

- source VCF file (see parameter 'source')
- output name prefix (see parameter 'prefix', optional)
- INFO key names (see parameter 'info_keys', optional)
- ID column name (see parameter 'id_column', optional)

Help and ChangeLog

The full parameter list and changelog can be found here.

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