/target/gpfs2/gcc/groups/gonl

Directory structure of data management for GoNL located on the Groningen cluster in /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
  • /CG
    • All Complete Genomics data for the samples that are part of GoNL2.
  • /FastQs?
    • All *.fq.gz files and lists of checksums for the rawdata of GoNL1 batches 1 through 6.
  • /batchX
    • /rawdata
      • here is optionally a list of symlinks to *.fq.gz files for this batch.
    • /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
  • /denovo_asm
    • denovo assembly
  • /downsampling
  • /extraAnnotation
  • /FastQs?
    • GoNL fastQ files, copied from Grid
  • /gonl_sampleBAM_md5sums.zip
    • MD5 sums from all sample BAM files found in /batchX/results/alignment/
  • /gvnl_2flowcells
    • DEPRECATED, 2 flowcell to be re-analysed
  • /gwas-chip
    • GWAS data used for QC
  • /imputationBenchmarking
    • data used for imputation, imputation benchmarking project, eQtl analysis, gold standard etc.
  • /imputation_BMImeta
    • BMI meta-analysis data
  • /LoF
    • Loss-of-Function variants
  • /RdamExome?
    • ???
  • /re-analysis2
    • all results for the re-analysis of 2 flowcells which have LQ reads in the second read of read pairs
  • /splitbams
    • ???
  • /SV
    • all Structural Variants detected per SV tool, also validation results included in this directory.
  • /targeted_denovo
    • ???
  • /trio-analysis
    • /intermediate
      • intermediate results
    • /rawdata
      • all trio-realigned BAM files
    • /resources
      • genotype data
    • /results
      • /snps
        • /releaseX
          • all releaseX GoNL SNP calls per chromosome
  • /unified_genotyper_indel_calls
    • indel calls made by Unified Genotyper (GATK)
  • /variantBurdenNonCodingRna
    • testdata for variant burden project
    • testdata for variant burden project