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SVVariantAnnotator walker

Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,993 admin
edited September 2012 in GenomeSTRiP Documentation

1. Introduction

The SVVariantAnnotator walker is a general framework for making different
annotations on VCF files containing structural variant records.

SVVariantAnnotator is conceptually similar to the GATK VariantAnnotator
walker, but is tailed for use with structural variations. Each annotator is
like a plug-in and you can run one or more annotators over the same file in
one invocation.

Each annotator can either add annotations (typically INFO fields) to the input
VCF file, or it can generate a textual report (e.g. tab delimited) for
additional processing, or it can generate one or more summary reports (also
text files) or all of the above. Different annotators may or may not support
all modes of operation.

2. Annotators

The following annotators are currently implemented:



3. Common Arguments

The following common arguments are handled by the SVVariantAnnotator walker

  • -A <annotation> : The name of the annotation(s) you want to run.

  • -B:variant,VCF ''input-vcf-file'' : The input VCF file is
    supplied to SVVariantAnnotator as a ROD binding using the generic GATK -B
    argument. : The input VCF file must be sorted in coordinate order based on the
    reference sequence.

  • -BTI variant : You should always pass this generic GATK flag when running
    SVVariantAnnotator to drive iteration over the input VCF file. Note that
    variant is literal.

  • -R '<reference-sequence> : Indexed fasta file containing the reference

  • -writeReport : Flag indicating that the annotator should print a report file
    (default false). : Typically, this will contain one line per VCF record and
    will contain the same information as the annotations that would be stored in
    the VCF file, but may be easier to parse.

  • -writeSummary : Flag indicating that the annotator should write a summary
    file (default false). : Depending on the annotator, the summary file produces
    information organized in different ways. : For example, the VariantsPerSample
    annotator produces a summary file containing a row for each sample and the
    count of variants in that sample.

  • -reportDirectory <directory> : The directory to write report files and
    summary files (default is the current directory).

  • -tempDir <directory> : The directory to use store temporary files.

4. Outputs

  • -O <output-file> : The destination for the output VCF file. : If you do
    not specify -O, then the annotator will not produce VCF annotations (but may
    produce reports or summaries).

  • -reportFile <file-path> : The path and file name for the report file. This
    overrides -reportDirectory. : If not supplied, the report file is based on the
    name of the annotator (and will be in the report directory).

  • -summaryFile <file-path> : The path and file name for the summary file.
    This overrides -reportDirectory : If not supplied, each annotator generates a
    default summary file name (if the annotator supports writing summary files).

5. Availability

Available in SVToolkit version 1.04.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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