| 18 | | |
| 19 | | === GoNL-level Directory structure === |
| 20 | | The root for all subsequent directories is /data/gcc/projects/gonl/ |
| 21 | | |
| 22 | | * /rawdata |
| 23 | | * Contains all the raw unprocessed data by batch |
| 24 | | * Ex: All raw data for the 1st batch is located in'' /data/gcc/projects/gonl/rawdata/first_batch/'' |
| 25 | | * /results |
| 26 | | * Contains all the results after processing the data |
| 27 | | * /results/BGI |
| 28 | | * Contains all the results from the BGI pipeline (snps, indels, metrics, etc.) |
| 29 | | * The XXX.snp.sorted.vcf files are sorted according to position. |
| 30 | | * The XXX.annotated.txt are the sorted files annotated from ANNOVAR. The options that were used for the annotation are: |
| 31 | | * --buildver hg18 |
| 32 | | * --annotationDirectory /data/gcc/tools/annovar_2011Jan31/annovar/humandb/ |
| 33 | | * --geneBasedAnnotations refgene,knowngene,ensgene |
| 34 | | * --regionBasedAnnotations band,segdup,dgv,gwascatalog |
| 35 | | * --filterBasedAnnotations snp130 |
| 36 | | |
| 37 | | Please refer to ANNOVAR website for a thorough description of the annotations: http://www.openbioinformatics.org/annovar/annovar_db.html |
| 38 | | |
| 39 | | |
| 40 | | * /results/immunochip |
| 41 | | * Contains all the results from the immunochip data (cleaned/QCed data, metrics, etc.) |
| 42 | | * /results/pipeline |
| 43 | | * Contains all the results from the sequence data through the GoNL pipeline by batch |
| 44 | | * Ex: Results on the first batch are in'' /gcc/data/projects/gonl/results/pipeline/first_batch'' |
| 45 | | * The subdirectory structure for each of the batches should be the following: |
| 46 | | * All results related to a sample shoud go in /sample_name |
| 47 | | * Ex: All results related to sample A2a (first batch) should go in'' /data/gcc/projects/gonl/results/pipeline/first_batch/A2a'' |
| 48 | | * All results related to a lane of a sample should go in /sample_name/lane_name |
| 49 | | * 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/ |
