Changes between Version 7 and Version 8 of DataManagement/ProjectData


Ignore:
Timestamp:
Jan 25, 2013 2:47:11 PM (8 years ago)
Author:
freerkvandijk
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • DataManagement/ProjectData

    v7 v8  
    2626     * /intermediate_results
    2727       * whatever is needed, will be empty at end of project
    28    * /gwas_data
     28   * /denovo_asm
     29     * denovo assembly
     30   * /downsampling
     31   * /extraAnnotation
     32   * /FastQs
     33     * GoNL fastQ files, copied from Grid
     34   * /gonl_sampleBAM_md5sums.zip
     35     * MD5 sums from all sample BAM files found in /batchX/results/alignment/
     36   * /gvnl_2flowcells
     37     * DEPRECATED, 2 flowcell to be re-analysed
     38   * /gwas-chip
     39     * GWAS data used for QC
     40   * /imputationBenchmarking
     41     * data used for imputation, imputation benchmarking project, eQtl analysis, gold standard etc.
     42   * /imputation_BMImeta
     43     * BMI meta-analysis data
     44   * /LoF
     45     * Loss-of-Function variants
     46   * /RdamExome
     47     * ???
     48   * /re-analysis2
     49     * all results for the re-analysis of 2 flowcells which have LQ reads in the second read of read pairs
     50   * /splitbams
     51     * ???
     52   * /SV
     53     * all Structural Variants detected per SV tool, also validation results included in this directory.
     54   * /targeted_denovo
     55     * ???
     56   * /trio-analysis
     57     * /intermediate
     58       * intermediate results
    2959     * /rawdata
    30        * original provided plink or genomestudio
     60       * all trio-realigned BAM files
     61     * /resources
     62       * genotype data
    3163     * /results
    32        * here the cleaned up genotypes in agreed upon format
    33      * /logs
    34    * /groningen_immunochip
    35      * /rawdata
    36      * /results
    37    * /pilot
    38      * /rawdata
    39        * /alignment
    40          * symlinks to the raw alignments used -> /first_batch/rawdata/some.aligned.cleaned.bam
    41      * /result
    42        * /snp
    43        * /indel
    44        * /cnv
    45      * logs
    46    * /bgi
    47      * /batchX
    48        * 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.
    49      * batchX/bam OR batchX/alignment
    50        * The BAM files aligned by BGI
    51      * batchX/CNV
    52        * CNVs in CNV Detector format. If you want to download for all samples, please download the compressed archive from batchX/
    53      * batchX/indel
    54        * !InDels in samtools pileup format. If you want to download for all samples, please download the compressed archive from batchX/
    55      * batchX/indel_annotation
    56        * Indels annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
    57      * batchX/SNP
    58        * SNP in SOAPsnp format. If you want to download for all samples, please download the compressed archive from batchX/
    59      * batchX/SNP_annotation
    60        * SNP annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
    61      * batchX/vcf_format/CNV
    62        * CNV in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    63      * batchX/vcf_format/indel
    64        * Indel in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    65      * batchX/vcf_format/SNP
    66        * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    67        * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    68        * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    69        * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
     64       * /snps
     65         * /releaseX
     66           * all releaseX GoNL SNP calls per chromosome
     67    * /unified_genotyper_indel_calls
     68      * indel calls made by Unified Genotyper (GATK)
     69    * /variantBurdenNonCodingRna
     70      * testdata for variant burden project