| 4 | | * DataManagement/ProjectData - how are rawdata, intermediate data and result data organized |
| 5 | | |
| 6 | | == UMCG SFTP (application20.target.rug.nl) == |
| 7 | | === raw_data === |
| 8 | | Contains all the data coming from BGI, including their variant calls. |
| 9 | | * /fastq |
| 10 | | ** A4 trio fasta files |
| 11 | | */hg18 |
| 12 | | ** Pilot snp, cnv, indel, stat files sent by BGI at the beginning of 2011 |
| 13 | | * /hg19 |
| 14 | | ** A4 trio bam, snp, cnv files sent by BGI in April 2011 |
| 15 | | |
| 16 | | === resources === |
| 17 | | * GoNL resources tarball (Thanks Freerk!) |
| 18 | | |
| 19 | | === results === |
| 20 | | Here is all the data that has gone through any kind processing at UMCG |
| 21 | | */bam/umcg/ |
| 22 | | ** A4 trio complete bam files |
| 23 | | ** pilot chromosomes 19, 20, X, Y, MT bam files |
| 24 | | * /snp/hg18 |
| 25 | | ** Pilot cleaned up VCF files from the BGI on hg18(sorted, updated to VCF4.0) |
| 26 | | * /snp/hg19 |
| 27 | | ** Pilot initial unfiltered calls from UMCG |
| 28 | | ** Lifted-over files from BGI |
| 29 | | |
| 30 | | == Millipede File Structure (millipede.service.rug.nl) == |
| 31 | | |
| 32 | | Important note: /data/gcc on millipede is soon to be discontinued and will be replaced by /target/gpfs2/gcc (accessible from both Millipede and Application20) |
| 33 | | === '''Access rights''' === |
| 34 | | * All data should only be writable by their owners |
| 35 | | * All tools and resources should be read/executable by the whole ''gcc'' group |
| 36 | | * All project-specific data and results should be read/executable by the ''gvnl'' group |
| | 4 | * DataManagement/ProjectData - how are rawdata, intermediate data and result data organized on the compute clusters |
| | 5 | * DataManagement/SftpServer - how to access the SFTP for data sharing |
