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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 Located in
EGAF00003287833 vcf.gz 170.0 MB
EGAF00003287834 vcf.gz 176.6 MB
EGAF00003287835 vcf.gz 183.0 MB
EGAF00003287858 vcf.gz 183.2 MB
EGAF00003287859 vcf.gz 182.3 MB
EGAF00003288029 vcf.gz 160.4 MB
EGAF00003288030 vcf.gz 164.7 MB
EGAF00003288034 vcf.gz 168.0 MB
EGAF00003288035 vcf.gz 174.4 MB
EGAF00003288038 vcf.gz 175.8 MB
EGAF00003288042 vcf.gz 226.2 MB
EGAF00003288044 vcf.gz 165.8 MB
EGAF00003288048 vcf.gz 174.8 MB
EGAF00003288058 vcf.gz 172.2 MB
EGAF00003288060 vcf.gz 168.7 MB
EGAF00003288063 vcf.gz 172.8 MB
EGAF00003288064 vcf.gz 177.5 MB
EGAF00003288068 vcf.gz 209.2 MB
EGAF00003288070 vcf.gz 169.6 MB
EGAF00003288075 vcf.gz 170.7 MB
EGAF00003288078 vcf.gz 179.3 MB
EGAF00003288082 vcf.gz 160.9 MB
EGAF00003288084 vcf.gz 162.5 MB
EGAF00003288085 vcf.gz 174.5 MB
EGAF00003288093 vcf.gz 166.1 MB
EGAF00003288100 vcf.gz 169.6 MB
EGAF00003288101 vcf.gz 164.1 MB
EGAF00003288105 vcf.gz 167.2 MB
EGAF00003288111 vcf.gz 172.5 MB
EGAF00003288114 vcf.gz 164.4 MB
EGAF00003288117 vcf.gz 164.8 MB
EGAF00003288515 vcf.gz 164.8 MB
EGAF00003289158 vcf.gz 174.7 MB
EGAF00003289163 vcf.gz 170.5 MB
EGAF00003289173 vcf.gz 165.3 MB
EGAF00003290588 vcf.gz 179.9 MB
EGAF00003290590 vcf.gz 167.7 MB
EGAF00003290591 vcf.gz 166.8 MB
EGAF00003290592 vcf.gz 182.1 MB
EGAF00003290595 vcf.gz 200.0 MB
EGAF00003290598 vcf.gz 188.1 MB
EGAF00003290599 vcf.gz 175.5 MB
EGAF00003290603 vcf.gz 174.3 MB
EGAF00003290609 vcf.gz 174.7 MB
EGAF00003292676 vcf.gz 169.1 MB
EGAF00003292691 vcf.gz 176.9 MB
EGAF00003292692 vcf.gz 175.6 MB
EGAF00003292695 vcf.gz 179.3 MB
EGAF00003292710 vcf.gz 165.8 MB
EGAF00003292713 vcf.gz 173.9 MB
EGAF00003292714 vcf.gz 174.6 MB
51 Files (8.9 GB)