GCContentAnnotator

Annotator that calculates local GC content for structual variants.

Category: Variant Annotators

The GCContent annotator is invoked through the SVAnnotator framework, which defines arguments common to all annotators.

Introduction

The GCContent annotator reports on the local GC content of the reference sequence underneath the structural variant.

Output Formats

This annotator can produce the following outputs: annotated VCF, report file.

The annotated VCF contains the following additional INFO fields:

GCFRACTION

The fraction of G or C bases on the reference sequence for this variant.

GCLENGTH

The length of this variant on the reference sequence (denominator for GC fraction).

The report file contains one line for each variant. The report file contains the following columns:

VARIANT

The ID of the variant.

CHR

The chromosome of the variant.

START

The start position of the variant.

END

The end position of the variant.

GCFRACTION

The fraction of G or C bases on the reference sequence for this variant.

GCLENGTH

The length of this variant on the reference sequence (denominator for GC fraction).

Example

 java -Xmx4g -cp SVToolkit.jar \
     org.broadinstitute.sv.main.SVAnnotator \
     -A GCContent \
     -R human_g1k_v37.fasta \
     -vcf input.vcf \
     -O output.vcf \
     -writeReport true \
     -reportDirectory reportdir

GCContentAnnotator specific arguments

There are no arguments specific to this annotator.