Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

457b9ff6-3710-475c-a86d-5a2b8c5fd0c6 - samples

ABSTRACT: Germline variants calls were defined using the sequenced reads derived from 230 patients with hepatocellular carcinoma. This dataset is comprised of one aggregated vcf file.

PROVIDER: EGAD00001009410 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Axiom Genome-Wide Chicken Array of Broiler Chickens

Project description:DNA was isolated from whole red blood cells from various lines and crosses of broiler chickens. DNA was genotyped using Axiom genome-wide chicken array and cel files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 using the software's Best Practices for agricultural animals. The results were exported (Genotyping_Data-3-21-2018.vcf) for all genotype calls and text file of all SNPs with >= 97% call rate rate was also produced for filtering the VCF file (ALL_SNPSs_with_Call_Rate_97_Plus_3-21-2018).

2019-05-25 | GSE131764 | GEO

Karlsson_et_al_OSA

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

5c3bae9e-5419-4598-869f-eed9a443bd1a - samples

Project description:Aggregated VCF file from cancer genes panel seq for the initial (n=500) cohort of solid tumors screened for the Basket of Baskets study

| EGAD00001008437 | EGA

c6b0cb6e-e6d9-4949-8ab9-e2ef9e817292 - samples

Project description:Patient-derived lung cancer organoids cram files : targeted seq 13 samples, whole exome seq 12 samples mutation profiles of PDO and matched tissue : aggregated vcf 1 file details : https://www.nature.com/articles/s41467-019-11867-6

| EGAD00001005317 | EGA

GATCI_WXS_germline - samples

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

A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [Tiling Array]

Project description:These are the tiling array data for the experiments describing LADs on murine chromosomes 5, 12, and 15 by Dam-ID, as determined by LMNB and EMD Dam tagging and detection experiments Supplemental Bed file contains GADA algorithm calls for genomic regions of chromosomes 5, 12 and 15 (-1= no lad, high confidence, 0=indeterminate, 1=LAD, high confidence)

2012-02-14 | GSE35777 | GEO

GATCI_germline_variants - samples

Project description:Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK Haplotype Caller, to generate germline variant calls across the SureSelect All Exon V5+UTR target region. Variant calls are in VCF format. In total there are samples from 173 donors. 101 donors have calls generated from both normal and tumour samples tumour samples, 94 of which have a matched normal. Details for the call can be found in the vcf headers.

| EGAD00001004127 | EGA

GATCI_WGS_germline.2 - samples

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

BRCA_SV - samples

Project description:structural variant calls from Delly, vcf format

| EGAD00001003754 | EGA

53c5f7c5-620a-4a44-bd46-fa0f2eae23b3 - samples

Project description:Panel-based next-generation sequencing data of 150 human surgical liver samples from Caucasian donors. The panel was designed for 340 ADME (absorption, distribution, metabolism and excretion) and ADME-related genes. NGS was carried out on the Illumina HiSeq2500 system (Illumina Inc., San Diego, CA, United States) at high depth with 2 × 100 bps paired-end reads. Variants were called using samtools and varscan (2.3.5). Data on n=15,727 filtered variants for the 150 patients are comprised in one vcf file.

| EGAD00001005116 | EGA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data