Changes between Version 5 and Version 6 of DataManagement


Ignore:
Timestamp:
Feb 9, 2011 11:20:33 AM (14 years ago)
Author:
a.kanterakis
Comment:

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  • DataManagement

    v5 v6  
    3030   * Contains all the results from the BGI pipeline (snps, indels, metrics, etc.)
    3131   * The XXX.snp.sorted.vcf files are sorted according to position.
     32   * The XXX.annotated.txt are the sorted files annotated from ANNOVAR. The options that were used for the annotation are:
     33       * --buildver hg18
     34       * --annotationDirectory /data/gcc/tools/annovar_2011Jan31/annovar/humandb/
     35       * --geneBasedAnnotations refgene,knowngene,ensgene
     36       * --regionBasedAnnotations band,segdup,dgv,gwascatalog
     37       * --filterBasedAnnotations snp130
     38       
     39       Please refer to ANNOVAR website for a thorough description of the annotations: http://www.openbioinformatics.org/annovar/annovar_db.html
     40
     41
    3242 * /results/immunochip
    3343   * Contains all the results from the immunochip data (cleaned/QCed data, metrics, etc.)