= /target/gpfs2/gcc/groups/gonl =
Directory structure of data management. On the Groningen cluster that would be target/gpfs2/gcc/groups/gonl  Permission to read by gonl group, some folders also write.

 * /tools
   * All software, scripts and tools used to process the data.
   * Note that all users can install tools of common interest in this shared directory; tools should specify version as typically multiple versions of the same tool cohabit.
 * /resources
   * All resources needed for data processing, including genome references, dbSNP releases, etc.
   * Note that all users can put resources of common interest here.
 * /home
   * one private folder per member of this group
 * /general
   * presentations, publications, other stuff
 * /projects
   * /batchX
     * /rawdata
       * here is a list of fq.gz files
     * /results
       * /alignment
         * here is a list of bam files
       * /stats
         * here is one file per QC tool
       * /snp
         * here is one vcf file per analysis run
     * /logs
     * /intermediate_results
       * whatever is needed, will be empty at end of project
   * /gwas_data
     * /rawdata
       * original provided plink or genomestudio
     * /results
       * here the cleaned up genotypes in agreed upon format
     * /logs
   * /groningen_immunochip
     * /rawdata
     * /results
   * /pilot
     * /rawdata
       * /alignment
         * symlinks to the raw alignments used -> /first_batch/rawdata/some.aligned.cleaned.bam
     * /result
       * /snp
       * /indel
       * /cnv
     * logs
   * /bgi
     * /batchX
       * A  set of compressed files containing the plain text data and  md5 files  for downloading purpose. These are named as follows:   timestamp.BGI.batchX.data_type.hg1X.data_format.tar.bz2. All plain text   data should be available as a compressed file, including but not  limited  to: CNV, !InDel, !InDel annotations, SNP, SNP annotation. Some of  these  are available in multiple formats; see [wiki:BGIDatasets BGI data] page for more explanation about the BGI data and its formats.md5 checksum files is also available for all files.
     * batchX/bam OR batchX/alignment
       * The BAM files aligned by BGI
     * batchX/CNV
       * CNVs in CNV Detector format. If you want to download for all samples, please download the compressed archive from batchX/
     * batchX/indel
       * !InDels in samtools pileup format. If you want to download for all samples, please download the compressed archive from batchX/
     * batchX/indel_annotation
       * Indels annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
     * batchX/SNP
       * SNP in SOAPsnp format. If you want to download for all samples, please download the compressed archive from batchX/
     * batchX/SNP_annotation
       * SNP annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
     * batchX/vcf_format/CNV
       * CNV in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
     * batchX/vcf_format/indel
       * Indel in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
     * batchX/vcf_format/SNP
       * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
       * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
       * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/