Table 1 List of GIAB datasets used for NeoMutate benchmarking. The data was downloaded in BAM format and converted back to fastq in order to fully test all the functionalities of the workflow. (WES: whole-exome sequencing; PE: paired-end)
From: NeoMutate: an ensemble machine learning framework for the prediction of somatic mutations in cancer
Sample ID | Lab | Project | Library type | Read length | Insert size | File format | Number of reads before trimming | Number of reads after trimming | % kept reads |
|---|---|---|---|---|---|---|---|---|---|
NA12878 | Broad Institute | CEU Trio Analysis (son) | WES, PE | 76 bp | 155 bp | BAM | 118,969,048 | 89,151,231 | 74.94 |
NA12891 | Broad Institute | CEU Trio Analysis (father) | WES, PE | 76 bp | 155 bp | BAM | 116,639,621 | 88,079,244 | 75.51 |
NA24631 | Oslo University Hospital | Asian (Han chinese) Trio (son) | WES, PE | 125 bp | 202 bp | BAM | 61,001,625 | 60,852,682 | 99.76 |