From d78e7f6c0a7603f7be9f5b2c06a9f473473689e6 Mon Sep 17 00:00:00 2001 From: weisburd Date: Fri, 2 Apr 2010 21:51:28 +0000 Subject: [PATCH] Added documentation. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3117 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/annotator/GenomicAnnotator.java | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java index 00326d8a8..784da2367 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java @@ -31,6 +31,37 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils; import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter; +/* + General documentation - todo put this in wiki? + + The GenomicAnnotator + + Input Files: + - Input files are specified using the -B,, arg. + + - One of the -B args should have the "variants" and contain the genotypes to be annotated. + + - Data files are also provided using the -B arg and should have be "table". + Table format: + - the coordinates must be position-based rather than offset-based (eg. 1-based half-open) + - special rows: + - can contain comment lines starting with # + - at the top of the file, there must be a header line of the form: + HEADER columnName1 columnName2 etc. TODO finalize this + - special columns: + - first column must be of the form chr:pos or chr:start-end. + - alt/ref haplotypes: + - if there is a column named "hap_ref", a variant will only be annotated with a given row if that row's "hap_ref" allele exactly matches the variant's reference sequence. + - + + + + + + + + + */ /** * Annotates variant calls with context information. Users can specify which of the available annotations to use.