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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Whole-Exome Sequencing Analysis of Tumor Biopsies from a Colorectal Cancer Patient

After the sequencing, reads were aligned against the reference human genome GRCh38 using Burrows-Wheeler Aligner (BWA, v0.7.12). SNVs and indels were called using MuTect2 (GATK 4.1.4.1). SNVs or indels with a VAF < 5% or those that were covered by fewer than three reads were discarded., iIf the SNVs were found in both components of one sample, a cut-off of two reads was applied. We further excluded variants identified in at least two of a panel of 210 non-tumor samples, including the non-tumor samples included in the current study. Variant annotation was performed by SnpEff software v.4.1.

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Data Access Policy of Datasets controlled by MF-DAC

ATTENTION: Please check the following policy and the documents/information to provide in order to get access to the requested datasets. You can find the governing policy on Zenodo under the link: https://zenodo.org/records/12517622 Please provide all information as requested in the document to the MF-DAC. Additionally, you can find more information about the Data Access Committee of the Medical Faculty of the University of Basel (MF-DAC) under the following link on Zenodo: https://zenodo.org/records/10137776

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
EGAS50000001385 Whole Genome Sequencing

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
EGAF50000486302 bam 17.5 GB
EGAF50000486303 bam 13.7 GB
EGAF50000486304 bam 17.3 GB
EGAF50000486305 bam 16.9 GB
EGAF50000486306 bam 18.0 GB
EGAF50000486307 xlsx 490.6 kB
6 Files (83.5 GB)