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Dataset developed for use with EOSC4Cancer of synthetic colorectal cancer tumor/normal pairs.

This dataset contains 10 tumor and normal pairs synthetic WGS data of colorectal cancer that were simulated in a standard format of Illumina paired-end reads. The NEAT read simulator (version 3.0, https://github.com/zstephens/neat-genreads) was utilized to synthetize these 10 pairs of tumor and normal WGS data. In the procedure of data generation, simulated parameters (i.e., sequencing error statistics, read fragment length distribution and GC% coverage bias) were learned from data models provided by NEAT. The average sequencing depth for tumor and normal samples aimed to reach around 110X and 60X, respectively. For generation of synthetic normal WGS data per each sample, a germline variant profile from a real patient was down-sampled randomly, representing 50% germline variants of a given patient. These were mixed with the other 50% in silico germline variants that were modelled randomly using an average mutation rate (0.001), finally constituting a full germline profile for normal synthetic WGS data. For generation of synthetic tumor WGS data per each sample, a pre-defined somatic short variant profile (SNVs+Indels) learnt from a real CRC patient was added to the germline variant profile used for creating the normal synthetic WGS data of the same patient, consisting of the variants for tumor sample. Neither copy number profile nor structural variation profile was introduced into the tumor synthetic WGS data. Tumor content and ploidy were assumed to be 100% and 2, respectively. For mapping/variant detection, the Sarek pipeline v3.1.2 (https://nf-co.re/sarek/3.1.2) was used, specifically: 1. BWA v0.7.17-r1188 for read mapping 2. GATK v4.3.0.0 for pre-processing BAM file (including markduplicates and recalibration). 2. Mutect2 (GATK v4.3.0.0) for somatic variant calling 3. Strelka2 v2.9.10 for germline and somatic variant calling Metadata information of 10 CRC patients used for the generation of synthetic normal and tumor WGS data: Patient_id Tumor_barcode Normal_barcode Age Sex Tissue Cancer SIM007 SIM007_T SIM007_N 71 F Rectal Primary CRC SIM008 SIM008_T SIM008_N 45 F Colon Neuroendocrine Metastasis CRC SIM010 SIM010_T SIM010_N 62 M Colon Metastasis CRC SIM011 SIM011_T SIM011_N 55 M Colon Neuroendocrine Metastasis CRC SIM012 SIM012_T SIM012_N 57 M Rectal Metastasis CRC SIM013 SIM013_T SIM013_N 69 M Colon Metastasis CRC SIM014 SIM014_T SIM014_N 68 M Colon Neuroendocrine primary CRC SIM015 SIM015_T SIM015_N 58 F Colon Primary CRC SIM016 SIM016_T SIM016_N 49 M Colon/Rectal Primary CRC SIM017 SIM017_T SIM017_N 78 M Colon Neuroendocrine primary CRC

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EGA public datasets

This policy is affiliated to the open access datasets archived at the EGA. Datasets are not subject to controlled access and, as a result, may be distributed without the requirement of a data access application.

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
EGAS50000000190 Synthetic Genomics
  • Changed file in one analysis
  • Dataset Released

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
EGAF50000127116 fastq.gz 12.0 GB
EGAF50000127117 fastq.gz 12.0 GB
EGAF50000127118 fastq.gz 12.0 GB
EGAF50000127119 fastq.gz 12.0 GB
EGAF50000127120 fastq.gz 11.9 GB
EGAF50000127121 fastq.gz 11.9 GB
EGAF50000127122 fastq.gz 11.9 GB
EGAF50000127123 fastq.gz 12.0 GB
EGAF50000127124 fastq.gz 6.5 GB
EGAF50000127125 fastq.gz 6.5 GB
EGAF50000127126 fastq.gz 11.9 GB
EGAF50000127127 fastq.gz 11.9 GB
EGAF50000127128 fastq.gz 11.9 GB
EGAF50000127129 fastq.gz 11.9 GB
EGAF50000127130 fastq.gz 12.0 GB
EGAF50000127131 fastq.gz 12.0 GB
EGAF50000127132 fastq.gz 6.6 GB
EGAF50000127133 fastq.gz 6.6 GB
EGAF50000127134 fastq.gz 6.5 GB
EGAF50000127135 fastq.gz 6.5 GB
EGAF50000127136 fastq.gz 6.5 GB
EGAF50000127137 fastq.gz 6.5 GB
EGAF50000127138 fastq.gz 6.5 GB
EGAF50000127139 fastq.gz 6.5 GB
EGAF50000127140 fastq.gz 6.5 GB
EGAF50000127141 fastq.gz 6.5 GB
EGAF50000127142 fastq.gz 12.0 GB
EGAF50000127143 fastq.gz 11.9 GB
EGAF50000127144 fastq.gz 11.9 GB
EGAF50000127145 fastq.gz 12.0 GB
EGAF50000127146 fastq.gz 12.0 GB
EGAF50000127147 fastq.gz 11.9 GB
EGAF50000127148 fastq.gz 6.6 GB
EGAF50000127151 fastq.gz 12.0 GB
EGAF50000127152 fastq.gz 12.0 GB
EGAF50000127153 fastq.gz 12.0 GB
EGAF50000127154 fastq.gz 12.0 GB
EGAF50000127155 fastq.gz 6.5 GB
EGAF50000127156 fastq.gz 12.0 GB
EGAF50000127157 fastq.gz 12.0 GB
EGAF50000127158 fastq.gz 12.0 GB
EGAF50000127159 fastq.gz 12.0 GB
EGAF50000127160 fastq.gz 6.6 GB
EGAF50000127161 fastq.gz 6.6 GB
EGAF50000127162 fastq.gz 6.6 GB
EGAF50000127163 fastq.gz 6.6 GB
EGAF50000127164 fastq.gz 6.6 GB
EGAF50000127165 fastq.gz 6.6 GB
EGAF50000127166 fastq.gz 6.6 GB
EGAF50000127167 fastq.gz 6.6 GB
EGAF50000127168 fastq.gz 6.6 GB
EGAF50000127169 fastq.gz 6.6 GB
EGAF50000127170 fastq.gz 6.6 GB
EGAF50000127171 fastq.gz 6.5 GB
EGAF50000127172 fastq.gz 6.5 GB
EGAF50000127173 fastq.gz 6.5 GB
EGAF50000127174 fastq.gz 6.5 GB
EGAF50000127175 fastq.gz 6.6 GB
EGAF50000127176 fastq.gz 6.6 GB
EGAF50000127177 fastq.gz 12.0 GB
EGAF50000127178 fastq.gz 12.0 GB
EGAF50000127179 fastq.gz 12.0 GB
EGAF50000127180 fastq.gz 12.0 GB
EGAF50000127181 fastq.gz 12.0 GB
EGAF50000127182 fastq.gz 12.0 GB
EGAF50000127183 fastq.gz 6.6 GB
EGAF50000127184 fastq.gz 6.6 GB
EGAF50000127185 fastq.gz 6.6 GB
EGAF50000127186 fastq.gz 6.6 GB
EGAF50000127187 fastq.gz 12.0 GB
EGAF50000127188 fastq.gz 12.0 GB
EGAF50000127189 fastq.gz 12.0 GB
EGAF50000127190 fastq.gz 12.0 GB
EGAF50000127191 fastq.gz 6.6 GB
EGAF50000127192 fastq.gz 6.6 GB
EGAF50000127193 fastq.gz 6.6 GB
EGAF50000127194 fastq.gz 6.6 GB
EGAF50000127195 fastq.gz 12.0 GB
EGAF50000127196 fastq.gz 12.0 GB
EGAF50000127197 fastq.gz 12.0 GB
EGAF50000127198 fastq.gz 12.0 GB
EGAF50000127199 fastq.gz 12.0 GB
EGAF50000127200 fastq.gz 12.0 GB
EGAF50000127201 fastq.gz 12.0 GB
EGAF50000127202 fastq.gz 12.0 GB
EGAF50000127203 fastq.gz 11.9 GB
EGAF50000127204 fastq.gz 6.5 GB
EGAF50000127205 fastq.gz 6.5 GB
EGAF50000127206 fastq.gz 6.5 GB
EGAF50000127207 fastq.gz 6.5 GB
EGAF50000127208 fastq.gz 6.6 GB
EGAF50000127209 fastq.gz 11.9 GB
EGAF50000127210 fastq.gz 11.9 GB
EGAF50000127211 fastq.gz 11.9 GB
EGAF50000127212 fastq.gz 11.9 GB
EGAF50000127213 fastq.gz 11.9 GB
EGAF50000127214 fastq.gz 11.9 GB
EGAF50000127215 fastq.gz 12.0 GB
EGAF50000127216 fastq.gz 6.6 GB
EGAF50000127218 fastq.gz 11.9 GB
EGAF50000127219 fastq.gz 6.6 GB
EGAF50000127220 fastq.gz 6.6 GB
EGAF50000127221 fastq.gz 6.6 GB
EGAF50000127222 fastq.gz 12.0 GB
EGAF50000127223 fastq.gz 12.0 GB
EGAF50000127224 fastq.gz 6.6 GB
EGAF50000127225 fastq.gz 6.6 GB
EGAF50000127226 fastq.gz 12.0 GB
EGAF50000127227 fastq.gz 12.0 GB
EGAF50000127228 fastq.gz 12.0 GB
EGAF50000127229 fastq.gz 12.0 GB
EGAF50000127230 fastq.gz 6.6 GB
EGAF50000127231 fastq.gz 6.6 GB
EGAF50000127232 fastq.gz 6.6 GB
EGAF50000127233 fastq.gz 6.6 GB
EGAF50000127234 fastq.gz 6.6 GB
EGAF50000127235 fastq.gz 6.6 GB
EGAF50000127236 fastq.gz 6.6 GB
EGAF50000127237 fastq.gz 6.6 GB
EGAF50000127238 fastq.gz 6.5 GB
EGAF50000127239 fastq.gz 6.5 GB
EGAF50000127240 fastq.gz 6.5 GB
EGAF50000127241 fastq.gz 6.5 GB
EGAF50000127242 fastq.gz 6.6 GB
EGAF50000127243 fastq.gz 6.6 GB
EGAF50000127244 fastq.gz 6.6 GB
EGAF50000127245 fastq.gz 6.6 GB
EGAF50000127246 fastq.gz 6.6 GB
EGAF50000127247 fastq.gz 6.6 GB
EGAF50000127248 fastq.gz 6.6 GB
EGAF50000127249 fastq.gz 6.6 GB
EGAF50000127250 fastq.gz 12.0 GB
EGAF50000127251 fastq.gz 12.0 GB
EGAF50000127252 fastq.gz 12.0 GB
EGAF50000127253 fastq.gz 12.0 GB
EGAF50000127269 fastq.gz 6.6 GB
EGAF50000127270 fastq.gz 6.6 GB
EGAF50000127271 fastq.gz 11.9 GB
EGAF50000127272 fastq.gz 11.9 GB
EGAF50000127273 fastq.gz 11.9 GB
EGAF50000127274 fastq.gz 12.0 GB
EGAF50000127275 fastq.gz 12.0 GB
EGAF50000127276 fastq.gz 12.0 GB
EGAF50000127277 fastq.gz 12.0 GB
EGAF50000127278 fastq.gz 12.0 GB
EGAF50000127279 fastq.gz 12.0 GB
EGAF50000127280 fastq.gz 12.0 GB
EGAF50000127281 fastq.gz 12.0 GB
EGAF50000127282 fastq.gz 12.0 GB
EGAF50000127283 fastq.gz 11.9 GB
EGAF50000127284 fastq.gz 6.5 GB
EGAF50000127285 fastq.gz 11.9 GB
EGAF50000127286 fastq.gz 11.9 GB
EGAF50000127287 fastq.gz 6.6 GB
EGAF50000127288 fastq.gz 6.6 GB
EGAF50000127289 fastq.gz 6.6 GB
EGAF50000127290 fastq.gz 6.6 GB
EGAF50000127291 fastq.gz 6.6 GB
EGAF50000127292 fastq.gz 6.6 GB
EGAF50000127293 fastq.gz 6.6 GB
EGAF50000127299 bai 8.8 MB
EGAF50000127300 bam 28.1 GB
EGAF50000127301 bai 8.8 MB
EGAF50000127302 bam 49.6 GB
EGAF50000127303 bai 8.9 MB
EGAF50000127304 bam 50.0 GB
EGAF50000127305 bai 8.8 MB
EGAF50000127306 bam 28.1 GB
EGAF50000127307 bam 28.4 GB
EGAF50000127308 bai 8.9 MB
EGAF50000127309 bam 50.0 GB
EGAF50000127310 bai 8.9 MB
EGAF50000127315 bam 49.6 GB
EGAF50000127316 bai 8.8 MB
EGAF50000127325 bai 8.9 MB
EGAF50000127326 bam 28.4 GB
EGAF50000127328 bai 8.9 MB
EGAF50000127329 bam 50.0 GB
EGAF50000127332 bam 50.0 GB
EGAF50000127333 bai 8.9 MB
EGAF50000127337 bai 8.9 MB
EGAF50000127338 bam 28.4 GB
EGAF50000127340 bai 8.9 MB
EGAF50000127341 bam 28.4 GB
EGAF50000127342 bai 8.8 MB
EGAF50000127343 bam 28.1 GB
EGAF50000127344 bai 8.9 MB
EGAF50000127345 bam 50.0 GB
EGAF50000127346 bai 8.9 MB
EGAF50000127347 bam 50.0 GB
EGAF50000127348 bai 8.9 MB
EGAF50000127349 bam 50.0 GB
EGAF50000127350 bam 28.4 GB
EGAF50000127351 bai 8.9 MB
EGAF50000127352 tbi 1.6 MB
EGAF50000127353 vcf.gz 30.1 MB
EGAF50000127354 vcf.gz 223.1 kB
EGAF50000127355 tbi 252.3 kB
EGAF50000127356 bai 8.9 MB
EGAF50000127357 bam 28.4 GB
EGAF50000127362 bai 8.8 MB
EGAF50000127363 bam 49.6 GB
EGAF50000127364 bai 8.9 MB
EGAF50000127365 bam 28.4 GB
EGAF50000127366 vcf.gz 193.3 kB
EGAF50000127367 tbi 222.3 kB
EGAF50000127368 tbi 1.6 MB
EGAF50000127369 vcf.gz 30.0 MB
EGAF50000127371 vcf.gz 229.6 kB
EGAF50000127372 tbi 244.6 kB
EGAF50000127373 tbi 1.6 MB
EGAF50000127374 vcf.gz 30.0 MB
EGAF50000127375 tbi 1.6 MB
EGAF50000127376 vcf.gz 30.1 MB
EGAF50000127377 vcf.gz 30.2 MB
EGAF50000127378 tbi 1.6 MB
EGAF50000127379 vcf.gz 953.1 kB
EGAF50000127380 tbi 754.8 kB
EGAF50000127381 vcf.gz 208.8 kB
EGAF50000127382 tbi 228.6 kB
EGAF50000127383 vcf.gz 30.1 MB
EGAF50000127384 tbi 1.6 MB
EGAF50000127385 vcf.gz 232.1 kB
EGAF50000127386 tbi 256.6 kB
EGAF50000127387 vcf.gz 30.1 MB
EGAF50000127388 tbi 1.6 MB
EGAF50000127389 vcf.gz 200.1 kB
EGAF50000127390 tbi 227.4 kB
EGAF50000127391 vcf.gz 141.8 kB
EGAF50000127392 tbi 175.2 kB
EGAF50000127393 vcf.gz 30.1 MB
EGAF50000127394 tbi 1.6 MB
EGAF50000127395 vcf.gz 30.0 MB
EGAF50000127396 tbi 1.6 MB
EGAF50000127397 vcf.gz 305.8 kB
EGAF50000127398 tbi 311.6 kB
EGAF50000127399 vcf.gz 30.0 MB
EGAF50000127400 tbi 1.6 MB
EGAF50000127401 vcf.gz 186.8 kB
EGAF50000127402 tbi 207.3 kB
EGAF50000129736 csv 605 Bytes
241 Files (2.3 TB)