| | 508 | * 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 |
| | 509 | * --pathToANNOVAR: The path to the installed ANNOVAR tool |
| | 510 | * --VCFFilename: The path to the VCF file to be annotated |
| | 511 | * --outputFilename: The output annotated file |
| | 512 | * --outputDirectory: output directory |
| | 513 | * --buildver: Could be either hg18 or hg18 |
| | 514 | * --annotationDirectory: The directory where the annotation files are |
| | 515 | * --geneBasedAnnotations: Gene Based Annotations according to ANNOVAR |
| | 516 | * --regionBasedAnnotations: Region Based Annotations according to ANNOVAR |
| | 517 | * --filterBasedAnnotations: Filter Based Annotations according to ANNOVAR |
| | 518 | * -- |
