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 somatic variants (MuTect)

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 MuTect to generate somatic 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
EGAF00003287860 vcf.gz 165.2 kB Report
EGAF00003287863 vcf.gz 10.9 MB Report
EGAF00003287865 vcf.gz 249.3 kB Report
EGAF00003287871 vcf.gz 648.6 kB Report
EGAF00003288031 vcf.gz 198.7 kB Report
EGAF00003288036 vcf.gz 113.5 kB Report
EGAF00003288039 vcf.gz 52.1 kB Report
EGAF00003288043 vcf.gz 217.0 kB Report
EGAF00003288045 vcf.gz 445.8 kB Report
EGAF00003288046 vcf.gz 288.2 kB Report
EGAF00003288049 vcf.gz 244.1 kB
EGAF00003288053 vcf.gz 145.1 kB Report
EGAF00003288055 vcf.gz 172.8 kB
EGAF00003288056 vcf.gz 217.6 kB Report
EGAF00003288059 vcf.gz 224.4 kB Report
EGAF00003288061 vcf.gz 91.2 kB Report
EGAF00003288062 vcf.gz 102.6 kB Report
EGAF00003288065 vcf.gz 451.4 kB Report
EGAF00003288069 vcf.gz 201.9 kB
EGAF00003288073 vcf.gz 140.4 kB Report
EGAF00003288076 vcf.gz 343.7 kB Report
EGAF00003288080 vcf.gz 852.5 kB Report
EGAF00003288086 vcf.gz 165.6 kB
EGAF00003288087 vcf.gz 200.1 kB Report
EGAF00003288088 vcf.gz 428.6 kB Report
EGAF00003288092 vcf.gz 313.2 kB Report
EGAF00003288098 vcf.gz 248.7 kB Report
EGAF00003288102 vcf.gz 196.1 kB Report
EGAF00003288103 vcf.gz 235.4 kB Report
EGAF00003288106 vcf.gz 221.6 kB Report
EGAF00003288107 vcf.gz 328.9 kB Report
EGAF00003288109 vcf.gz 328.5 kB Report
EGAF00003288112 vcf.gz 172.9 kB Report
EGAF00003288115 vcf.gz 100.1 kB Report
EGAF00003288118 vcf.gz 169.1 kB Report
EGAF00003288119 vcf.gz 171.7 kB Report
EGAF00003289156 vcf.gz 348.7 kB Report
EGAF00003289159 vcf.gz 124.3 kB Report
EGAF00003289161 vcf.gz 111.2 kB Report
EGAF00003290593 vcf.gz 199.1 kB Report
EGAF00003290600 vcf.gz 195.2 kB
EGAF00003290601 vcf.gz 697.7 kB Report
EGAF00003290604 vcf.gz 236.0 kB Report
EGAF00003290605 vcf.gz 292.7 kB Report
EGAF00003290606 vcf.gz 198.4 kB Report
EGAF00003290610 vcf.gz 160.0 kB Report
EGAF00003290612 vcf.gz 696.9 kB Report
EGAF00003290614 vcf.gz 147.5 kB Report
EGAF00003292677 vcf.gz 136.4 kB Report
EGAF00003292681 vcf.gz 501.5 kB Report
EGAF00003292689 vcf.gz 109.3 kB Report
EGAF00003292690 vcf.gz 112.4 kB Report
EGAF00003292702 vcf.gz 84.0 kB Report
EGAF00003292711 vcf.gz 192.3 kB Report
EGAF00003292715 vcf.gz 463.7 kB Report
EGAF00003292722 vcf.gz 999.5 kB Report
EGAF00003292727 vcf.gz 461.6 kB Report
EGAF00003292728 vcf.gz 427.2 kB Report
EGAF00003292820 vcf.gz 103.6 kB Report
EGAF00003292821 vcf.gz 68.3 kB Report
60 Files (26.8 MB)