| 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 |
| 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 |
