= /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