SVVariantAnnotator walker
GenomeSTRiP Documentation | Created 2012-09-12 | Last updated 2012-09-21

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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 itself:

  • -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 sequence.

  • -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.

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