This page is work-in-progress regarding the data Management of the GoNL.

UMCG SFTP (application20.target.rug.nl)

raw_data

Contains all the data coming from BGI, including their variant calls.

• /fastq

A4 trio fasta files */hg18 Pilot snp, cnv, indel, stat files sent by BGI at the beginning of 2011

• /hg19

A4 trio bam, snp, cnv files sent by BGI in April 2011

resources

• GoNL resources tarball (Thanks Freerk!)

results

Here is all the data that has gone through any kind processing at UMCG */bam/umcg/ A4 trio complete bam files pilot chromosomes 19, 20, X, Y, MT bam files

• /snp/hg18

Pilot cleaned up VCF files from the BGI on hg18(sorted, updated to VCF4.0)

• /snp/hg19

Pilot initial unfiltered calls from UMCG Lifted-over files from BGI

Millipede File Structure (millipede.service.rug.nl)

Access rights

• All data should only be writable by their owners
• All tools and resources should be read/executable by the whole gcc group
• All project-specific data and results should be read/executable by the gvnl group

GCC-level Directory Structure

The root for all subsequent directories is data/gcc/

• /tools
  • Contains all GCC tools including GoNL tools
  • All tools should be put in a folder using the naming convention: toolname-version
    • Ex: Picard v1.32 should be found in /data/gcc/tools/picard-tools-1.32/
• /resources
  • Contains all GCC resources inlcluding GoNL resources
  • All resources should be put in a folder precising their version. Normally, should follow resource-version.
    • Ex: Human Genome build 19 should be found in /data/gcc/resources/hg-19/

GoNL-level Directory structure

The root for all subsequent directories is /data/gcc/projects/gonl/

• /rawdata
  • Contains all the raw unprocessed data by batch
    • Ex: All raw data for the 1st batch is located in /data/gcc/projects/gonl/rawdata/first_batch/
• /results
  • Contains all the results after processing the data
• /results/BGI
  • Contains all the results from the BGI pipeline (snps, indels, metrics, etc.)
  • The XXX.snp.sorted.vcf files are sorted according to position.
  • The XXX.annotated.txt are the sorted files annotated from ANNOVAR. The options that were used for the annotation are:
    • --buildver hg18
    • --annotationDirectory /data/gcc/tools/annovar_2011Jan31/annovar/humandb/
    • --geneBasedAnnotations refgene,knowngene,ensgene
    • --regionBasedAnnotations band,segdup,dgv,gwascatalog
    • --filterBasedAnnotations snp130

Please refer to ANNOVAR website for a thorough description of the annotations: ​http://www.openbioinformatics.org/annovar/annovar_db.html

• /results/immunochip
  • Contains all the results from the immunochip data (cleaned/QCed data, metrics, etc.)
• /results/pipeline
  • Contains all the results from the sequence data through the GoNL pipeline by batch
    • Ex: Results on the first batch are in /gcc/data/projects/gonl/results/pipeline/first_batch
  • The subdirectory structure for each of the batches should be the following:
    • All results related to a sample shoud go in /sample_name
      • Ex: All results related to sample A2a (first batch) should go in /data/gcc/projects/gonl/results/pipeline/first_batch/A2a
    • All results related to a lane of a sample should go in /sample_name/lane_name
      • Ex: All results related to sample A2a (first batch), Lane FC20005_L1 should go in /data/gcc/projects/gonl/results/pipeline/first_batch/A2a/FC20005_L1/

Pipeline Result Files Naming Convention

The following convention applies to all files that are generated by the pipeline. For containing folders, see sections above.

• General convention
  • Filenames are composed of tokens identifying their content. The tokens are separated by '.' and if necessary the words within the tokens can be separated by '_' for reading purpose.
  • Except where it references specific names using another convention (ex: sample name), file names should be all small letters.
• Sample-level files should be named using: sample_name.step_id.step_name.genome_build.time_stamp.extension
  • Ex: A vcf file for the sample A2a produced by the step vc02 (step 2 of variant calling) with the tool UnifiedGenotyper using genome build human_g1k_v37 on a run that begun on February 1st 2011 at 12:00 should be named: A2a.vc02.unified_genotyper.human_g1k_v37.2011_02_01_12_00.snp
• Lane-level files should be named using: sample_name.lane_name.step_id.step_name.genome_build.time_stamp.extension
  • Ex: A bam file for the lane FC20005_L1 of the sample A2a produced by the step pe03 (step 3 of paired-end alignment) with the tool BWA sampe using genome build human_g1k_v37 on a run that begun on February 1st 2011 at 12:00 should be named: A2a.FC20005_L1.pe03.bwa_sampe.human_g1k_v37.2011_02_12_00.bam
• Log file names should correspond to their output counterparts and have the .log extension.
  • Ex: log file for the vcf sample-level step above should be: A2a.vc02.unified_genotyper.human_g1k_v37.2011_02_01_12_00.log
  • Ex: log file for the bam lane-level step above should be: A2a.FC20005_L1.pe03.bwa_sampe.human_g1k_v37.2011_02_12_00.log

Logging

The logging strategy is currently under development but will be composed of both file logs and database entries in a Molgenis platform. The status is described below.

Log Files

• At each step of the pipeline a single log is produced and contains:
  • PBS out and err
  • Tool out and err
  • Other tool-produced log where applicable
• For log file naming, see section above.

Molgenis

The Molgenis platform will be used to provide a more advanced and general view of the status of the pipeline runs (including different views, sorting, etc.) The current status is:

• Molgenis instance created with proposed model
• Scripts for insertion under development