About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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GATCI whole genome germline variants

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

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Data Access Agreement for the Nichols Group

Data will be available to qualified investigators upon request.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001002234 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
i
EGAF00003287833 vcf.gz 170.0 MB Report
EGAF00003287834 vcf.gz 176.6 MB Report
EGAF00003287835 vcf.gz 183.0 MB Report
EGAF00003287858 vcf.gz 183.2 MB Report
EGAF00003287859 vcf.gz 182.3 MB Report
EGAF00003288029 vcf.gz 160.4 MB Report
EGAF00003288030 vcf.gz 164.7 MB Report
EGAF00003288034 vcf.gz 168.0 MB Report
EGAF00003288035 vcf.gz 174.4 MB Report
EGAF00003288038 vcf.gz 175.8 MB Report
EGAF00003288042 vcf.gz 226.2 MB Report
EGAF00003288044 vcf.gz 165.8 MB Report
EGAF00003288047 vcf.gz 175.7 MB Report
EGAF00003288048 vcf.gz 174.8 MB Report
EGAF00003288058 vcf.gz 172.2 MB Report
EGAF00003288060 vcf.gz 168.7 MB Report
EGAF00003288063 vcf.gz 172.8 MB Report
EGAF00003288064 vcf.gz 177.5 MB Report
EGAF00003288068 vcf.gz 209.2 MB Report
EGAF00003288070 vcf.gz 169.6 MB Report
EGAF00003288072 vcf.gz 174.9 MB Report
EGAF00003288075 vcf.gz 170.7 MB Report
EGAF00003288078 vcf.gz 179.3 MB Report
EGAF00003288081 vcf.gz 164.4 MB Report
EGAF00003288082 vcf.gz 160.9 MB Report
EGAF00003288084 vcf.gz 162.5 MB Report
EGAF00003288085 vcf.gz 174.5 MB Report
EGAF00003288093 vcf.gz 166.1 MB Report
EGAF00003288095 vcf.gz 176.1 MB Report
EGAF00003288100 vcf.gz 169.6 MB Report
EGAF00003288101 vcf.gz 164.1 MB Report
EGAF00003288104 vcf.gz 167.3 MB Report
EGAF00003288105 vcf.gz 167.2 MB Report
EGAF00003288111 vcf.gz 172.5 MB Report
EGAF00003288114 vcf.gz 164.4 MB Report
EGAF00003288117 vcf.gz 164.8 MB Report
EGAF00003288511 vcf.gz 165.2 MB Report
EGAF00003288512 vcf.gz 165.2 MB Report
EGAF00003288513 vcf.gz 165.5 MB Report
EGAF00003288514 vcf.gz 165.5 MB Report
EGAF00003288515 vcf.gz 164.8 MB Report
EGAF00003289158 vcf.gz 174.7 MB Report
EGAF00003289163 vcf.gz 170.5 MB Report
EGAF00003289173 vcf.gz 165.3 MB Report
EGAF00003290588 vcf.gz 179.9 MB Report
EGAF00003290590 vcf.gz 167.7 MB Report
EGAF00003290591 vcf.gz 166.8 MB Report
EGAF00003290592 vcf.gz 182.1 MB Report
EGAF00003290595 vcf.gz 200.0 MB Report
EGAF00003290598 vcf.gz 188.1 MB Report
EGAF00003290599 vcf.gz 175.5 MB Report
EGAF00003290603 vcf.gz 174.3 MB Report
EGAF00003290609 vcf.gz 174.7 MB Report
EGAF00003292676 vcf.gz 169.1 MB Report
EGAF00003292691 vcf.gz 176.9 MB Report
EGAF00003292692 vcf.gz 175.6 MB Report
EGAF00003292695 vcf.gz 179.3 MB Report
EGAF00003292710 vcf.gz 165.8 MB Report
EGAF00003292713 vcf.gz 173.9 MB Report
EGAF00003292714 vcf.gz 174.6 MB Report
60 Files (10.4 GB)