Analyses_Dataset - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001010138 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This experiment was conducted to generate targeted resequencing data covering a region associated with osteosarcoma in greyhounds. 8 greyhounds diagnosed with osteosarcoma and 7 greyhounds without tumors were sequenced. DNA from the 15 dogs was used to prepare libraries and hybrid capture performed to enrich the region of interest prior to paired-end sequencing using Illumina Genome Analyzer II. The reads were aligned to the dog-genome CanFam2.0 using bwa and pre-processed using Picard and GATK. Variant discovery was performed using GATK. The resulting list of variants were used in the study to finemap the associated region and look for causal variants. We submit the preprocessed BAM-files that still have all reads although some reads are flagged. We also submit the resulting vcf-file with called and filtered variants in all individuals.
2013-11-16 | E-MTAB-1984 | biostudies-arrayexpress
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress
Project description:Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/MuTect, to generate somatic variant calls across the SureSelect All Exon V5+UTR target region. Somatic variant calls are in VCF format. In total there are 166 tumour samples, 94 of which have a matched normal. Somatic variants for tumours without a matched normal, were called against a panel of normals. Details for the mutect call can be found in the vcf header.
| EGAD00001004129 | EGA
Project description:Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK Haplotype Caller to generate germline variant calls. Variant calls are in VCF format. Details for the call can be found in the VCF header
| EGAD00001005916 | EGA
Project description:Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/SomaticSniper, to generate somatic variant calls. Somatic variant calls are in VCF format. Details for the mutect call can be found in the vcf header.
| EGAD00001005918 | EGA
Project description:Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/MuTect, to generate somatic variant calls. Somatic variant calls are in VCF format. Details for the mutect call can be found in the vcf header.
| EGAD00001005917 | EGA
Project description:<p>Genetic analysis of patients with Inherited Retinal Dystrophies (IRDs) was carried out by performing Whole Genome Sequencing (WGS). The main purpose of this study is to identify simple and complex mutations responsible for IRD in patients. </p> <p>WGS was performed on selected affected and unaffected individuals using the Illumina HiSeqX10. The reads were aligned to human genome 19 (hg19) and variant calling was performed using Genome Analysis Toolkit (GATK). The genotyping quality of single nucleotide variants (SNVs) and indels was assessed using the variant quality score recalibration approach implemented in GATK. Copy number variations (CNVs) were called using Genome STRiP and SpeedSeq. </p> <p>This large set of whole genome sequencing data from different ethnicity can be stored and shared through dbGaP. This data could serve as a source for checking frequencies of variants or the pathogenicity of selected variants in different ethnicities. </p>
| phs001619 | dbGaP
Project description:Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM and preprocessed with GATK for indel realignment and base quality score recalibration. Aligned sequence was analyzed with GATK HaplotypeCaller to generate germline variant calls. Variant calls are in VCF format. In total, there are 60 tumour samples from 38 patients, all with matched normal. Further details can be found in the vcf headers
| EGAD00001005817 | EGA
Project description:<p><b>LOCATION CHANGE FOR ALZHEIMER'S DISEASE SEQUENCING PROJECT (ADSP) DATA:</b> Please go to <a href="https://dss.niagads.org/" target="_blank">NIAGADS DSS</a> to apply for build 38 ADSP genetic and phenotypic data. See Background below for more details. For instructions on how to access the additional ADSP data that are shared through <a href="https://dss.niagads.org/" target="_blank">NIAGADS DSS</a>, visit the <a href="https://dss.niagads.org/documentation/" target="_blank">Application Instructions</a> page.</p> <p>Background: Additional sequencing data are continuously being generated by the ADSP. These data are mapped to the latest Genome Reference Consortium human genome build GRCh38 (hg38) and are being shared through the NIA Genetics of Alzheimer's Disease Data Storage Site (<a href="https://www.niagads.org/" target="_blank">NIAGADS</a>) Data Sharing Service (<a href="https://dss.niagads.org/" target="_blank">DSS</a>). As of May 1, 2020 there are 4,789 whole genomes and 19,922 whole exomes available to the research community. Later in 2020 there will be a total of ~17,000 whole genomes and 19,922 whole exomes available through NIAGADS DSS (<a href="https://dss.niagads.org/datasets/ng00067/" target="_blank">ng00067</a>). The total number of genomes from multi-ethnic cohorts is anticipated to exceed 50,000. Please see the <a href="https://www.niagads.org/adsp/content/study-design">ADSP Design</a> page for the complete study description.</p> <p>ADSP whole exome and whole genome sequence data that were shared through dbGaP were mapped to the GRCh37 (build 37). These data are from the Discovery Phase of the project (described below) and will continue to be available at this site.</p> <p><b>STUDY DESCRIPTION FOR dbGaP BUILD 37 ADSP DATA: </b>The overarching goals of the Alzheimer's Disease Sequencing Project (ADSP) are to: (1) identify new genomic variants contributing to increased risk of developing Alzheimer's Disease (AD), (2) identify new genomic variants contributing to protection against developing AD, and (3) provide insight as to why individuals with known risk factor variants escape from developing AD. These factors will be studied in multi-ethnic populations in order to identify new pathways for disease prevention. Such a study of human genomic variation and its relationship to health and disease requires examination of a large number of study participants and needs to capture information about common and rare variants (both single nucleotide and copy number) in well phenotyped individuals.</p> <p>Using existing samples from NIH funded and other studies, three NHGRI funded Large Scale Sequencing and Analysis Centers (LSAC) - Broad, Baylor, and Washington University - produced the DNA sequence data. Variant call data are being made available to the scientific community through NIH-approved data repositories. Statistical analysis of the sequence data is anticipated to identify new genetic risk and protective factors. The ADSP will conduct and facilitate analysis of sequence data to extend previous discoveries that may ultimately result in new directions for AD therapeutics. Analysis of ADSP data will be done in two phases.</p> <p>The Discovery Phase analysis (2014-2018) is funded under <a href="http://grants.nih.gov/grants/guide/pa-files/PAR-12-183.html">PAR-12-183</a>. The entire Discovery dataset contains whole-genome sequencing data on 584 subjects from 113 families, and pedigree data for > 4000 subjects; whole exome sequencing data on 5096 cases 4965 controls; and whole exome sequence data on an additional 853 (682 Cases [510 Non-Hispanic, 172 Hispanic]), and 171 Hispanic Control subjects from families that are multiply affected with AD.</p> <p>The Replication Phase (2016-2021) analysis will be funded under <a href="http://grants.nih.gov/grants/guide/rfa-files/RFA-AG-16-001.html">RFA-AG-16-001</a> and <a href="http://grants.nih.gov/grants/guide/rfa-files/RFA-AG-16-002.html">RFA-AG-16-002</a> and is expected to include a combination of genotyping and sequencing approaches on at least 30,000 subjects. Targeted sequencing will be done by the LSACs.</p> <p><b>GRCh37 Data Releases</b></p> <ul> <li>The <b>first</b> ADSP data release occurred on November 25, 2013. It included the whole-genome sequencing data in BAM file format on 410 individuals.</li> <li>The <b>second</b> ADSP data release occurred on March 31, 2014, and included the whole-genome sequencing data in BAM file format for an additional 168 individuals.</li> <li>The <b>third</b> ADSP data release occurred on November 03, 2014 and included whole-exome sequencing data in BAM file format for 10,939 individuals.</li> <li>The <b>fourth</b> ADSP data release occurred on February 13, 2015 and included revised ethnic data for subjects with whole-exome sequencing data.</li> <li>The <b>fifth</b> ADSP data release occurred on July 13, 2015 and included whole-genome genotypes and updated phenotypes as well as changes to pedigree structures and sample IDs.</li> <li>The <b>sixth</b> ADSP data release occurred on December 8, 2015, and included whole-exome genotypes and updated phenotypes as well as changes to subject IDs.</li> </ul> <p>This <b>seventh ADSP data release on April 12, 2016</b> includes: </p> <ul> <p>(1) WES and WGS SNV VCF files</p> <p>(2) WES and WGS Indel PLINK files</p> </ul> <p><b>ADSP Data Available through dbGaP:</b></p> <p> <table border="1"> <tr> <th></th> <th><b>ADSP - Whole Genome Sequencing</b></th> <th><b>ADSP - Whole Exome Sequencing</b></th> <th><b>Comments</b></th> </tr> <tr> <td>DNA-Seq (BAM)</td> <td>n=578</td> <td>n=10913</td> <td>Sequence data available (plus n=38 replications w/out genotype data)</td> </tr> <tr> <td>Concordant SNV Genotypes (PLINK format)</td> <td>N/A</td> <td>n=10913</td> <td>QC'ed genotypes that are concordant between the Atlas (Baylor's) and GATK (Broad's) calling pipelines (a subset of the consensus genotype set)</td> </tr> <tr> <td>Consensus Genotypes (PLINK and VCF format)</td> <td>n=578</td> <td>n=10913</td> <td>QC'ed genotypes that are concordant between Atlas and GATK pipelines as well as those that that were called uniquely by Atlas or GATK</td> </tr> <tr> <td>Concordant Indel Genotypes (PLINK format)</td> <td>n=578</td> <td>n=10913</td> <td>QC'ed genotypes that are concordant between the Atlas and GATK calling pipelines</td> </tr> <tr> <td>Phenotype Data</td> <td>n=4735</td> <td>n=10913</td> <td>Data of n=53 phenotype variables available (plus administrative data), including APOE genotype. WGS phenotypes include data of connecting family members.</td> </tr> </table> </p> <p>Please use the <a href="ftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000572/phs000572.v7.p4/">release notes</a> provided by dbGaP to obtain detailed information about study release updates. </p> <p>The <a href="https://www.niagads.org/adsp/portal/">ADSP data portal</a> provides a customized interface for users to quickly identify and retrieve files by covariates, phenotypes, and data properties such as sequencing facility or coverage. For more information about the ADSP study and the data portal, please visit <a href="https://www.niagads.org/adsp/">https://www.niagads.org/adsp/</a>.</p>
| phs000572 | dbGaP
Project description:Variants on the Y chromosome for 62 danish males in VCF format from the GenomeDenmark Phase 2 cohort. Variants were called using reference based approaches such as the haplotype-caller module from GATK and using alignment of denovo assemblies to the reference using ASMvar.
| EGAD00001003186 | EGA