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 (SomaticSniper)

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 SomaticSniper 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
EGAF00003287857 vcf.gz 78.4 kB Report
EGAF00003287864 vcf.gz 16.6 MB Report
EGAF00003287866 vcf.gz 211.8 kB Report
EGAF00003287872 vcf.gz 760.5 kB Report
EGAF00003288028 vcf.gz 136.1 kB Report
EGAF00003288032 vcf.gz 45.3 kB Report
EGAF00003288033 vcf.gz 231.0 kB Report
EGAF00003288037 vcf.gz 468.6 kB
EGAF00003288040 vcf.gz 46.2 kB
EGAF00003288041 vcf.gz 48.7 kB
EGAF00003288050 vcf.gz 66.6 kB Report
EGAF00003288051 vcf.gz 88.0 kB Report
EGAF00003288052 vcf.gz 203.4 kB Report
EGAF00003288054 vcf.gz 59.7 kB Report
EGAF00003288057 vcf.gz 204.9 kB Report
EGAF00003288066 vcf.gz 21.5 kB Report
EGAF00003288067 vcf.gz 413.8 kB Report
EGAF00003288071 vcf.gz 118.2 kB Report
EGAF00003288074 vcf.gz 106.7 kB Report
EGAF00003288077 vcf.gz 259.0 kB Report
EGAF00003288079 vcf.gz 171.5 kB Report
EGAF00003288083 vcf.gz 132.2 kB Report
EGAF00003288089 vcf.gz 46.0 kB Report
EGAF00003288090 vcf.gz 111.6 kB Report
EGAF00003288091 vcf.gz 287.0 kB Report
EGAF00003288094 vcf.gz 121.5 kB Report
EGAF00003288096 vcf.gz 71.6 kB Report
EGAF00003288097 vcf.gz 23.9 kB Report
EGAF00003288099 vcf.gz 121.3 kB Report
EGAF00003288108 vcf.gz 210.9 kB Report
EGAF00003288110 vcf.gz 58.0 kB Report
EGAF00003288113 vcf.gz 110.5 kB Report
EGAF00003288116 vcf.gz 59.7 kB Report
EGAF00003288120 vcf.gz 50.6 kB Report
EGAF00003288505 vcf.gz 110.8 kB Report
EGAF00003288509 vcf.gz 69.9 kB Report
EGAF00003288510 vcf.gz 125.9 kB Report
EGAF00003289157 vcf.gz 314.9 kB Report
EGAF00003289160 vcf.gz 96.9 kB Report
EGAF00003289162 vcf.gz 26.1 kB Report
EGAF00003289164 vcf.gz 21.4 kB Report
EGAF00003289165 vcf.gz 80.0 kB Report
EGAF00003289166 vcf.gz 23.2 kB Report
EGAF00003289167 vcf.gz 27.2 kB Report
EGAF00003290594 vcf.gz 128.8 kB Report
EGAF00003290596 vcf.gz 272.5 kB
EGAF00003290597 vcf.gz 1.0 MB Report
EGAF00003290602 vcf.gz 725.9 kB
EGAF00003290607 vcf.gz 131.1 kB Report
EGAF00003290608 vcf.gz 142.0 kB Report
EGAF00003290611 vcf.gz 268.3 kB Report
EGAF00003290615 vcf.gz 63.0 kB Report
EGAF00003290616 vcf.gz 145.7 kB Report
EGAF00003292682 vcf.gz 530.9 kB Report
EGAF00003292683 vcf.gz 462.6 kB Report
EGAF00003292684 vcf.gz 304.4 kB Report
EGAF00003292685 vcf.gz 517.9 kB Report
EGAF00003292694 vcf.gz 169.8 kB Report
EGAF00003292709 vcf.gz 87.2 kB Report
EGAF00003292712 vcf.gz 35.1 kB Report
60 Files (27.6 MB)