Changes between Version 24 and Version 25 of SnpAnnotationPipeline

Timestamp:

Jan 5, 2011 11:58:54 AM (13 years ago)

Author:

a.kanterakis

Comment:

--

SnpAnnotationPipeline

@@ -507 +507 @@
  * Usage:
  * Example: python ANNOVAR.py --pathToANNOVAR /data/home/akanterakis/tools/ANNOVAR/annovar  --VCFFilename /data/home/data/pdeelen/Celiac40ExomsProject/SequenceData/sequence0605_41.index_hg18.snps.filtered.vcf --outputFilename /data/home/data/alex/ANNOVAR/annotated/output.txt --outputDirectory /data/home/data/alex/ANNOVAR/annotated/ --buildver hg18 --annotationDirectory /data/home/data/alex/ANNOVAR/humandb_hg18/ --geneBasedAnnotations refgene,knowngene,ensgene --regionBasedAnnotations band,segdup,dgv,gwascatalog --filterBasedAnnotations snp130 --customAnnotations kantale
+ * Options:
     * --pathToANNOVAR: The path to the installed ANNOVAR tool
     * --VCFFilename: The path to the VCF file to be annotated
@@ -513 +514 @@
     * --buildver: Could be either hg18 or hg18
     * --annotationDirectory: The directory where the annotation files are
-    * --geneBasedAnnotations: Gene Based Annotations according to ANNOVAR
-    * --regionBasedAnnotations: Region Based Annotations according to ANNOVAR
-    * --filterBasedAnnotations: Filter Based Annotations according to ANNOVAR
+    * --geneBasedAnnotations: Gene Based Annotations according to ANNOVAR (coma separated no spaces)
+    * --regionBasedAnnotations: Region Based Annotations according to ANNOVAR (coma separated no spaces)
+    * --filterBasedAnnotations: Filter Based Annotations according to ANNOVAR (coma separated no spaces)
+    * --customAnnotations: Custom annotations. These should be GFF3 files http://www.sequenceontology.org/gff3.shtml. The list of files should be comma separated no spaces
+    * --dummy: If set True, the script will not do anything just print the script commands. Default value: False
     * --
 = Related work =