Annotation Comparison

These data are supplementary to the paper: McCarthy, DJ et al. Choice of transcripts and software has a large effect on variant annotation. Genome Medicine. 2014, 6:26. doi:10.1186/gm543 http://genomemedicine.com/content/6/3/26/abstract Variant annotation is a fundamental step in the analysis of genome sequence data. However, annotation results can vary widely depending on the transcript sets and software tools used to obtain annotations. This dataset was designed to investigate the extent of difference in annotations due to use of different transcript sets and different software tools. We recommend starting with the README.md file, which describes the contents of the two large data files. The archive source_code_for_mccarthy_et_al_2014_gm_anno_comparison.tar contains that the source code that was used to produce the results presented in the paper cited above. The two large files are gzipped, tab-delimited files containing details of annotations for 80 million DNA variants from a whole-genome sequencing study. The file union_rfs_ens_comparison_with_tx.tab.gz contains annotions using the RefSeq (version 57) and Ensembl (version 69) transcript sets obtained with the annotation package Annovar (version of Feb 2013). This dataset can be used to investigate the differences in annotation that arise when using these two transcript sets. The file ANV_VEP_ens_comparison_best_annos.tab.gz contains annotations using the Ensembl (version 69) transcript set, but different software tools: Annovar (version of Feb 2013) and Ensembl's Variant Effect Predictor (VEP; version 2.7). This dataset can be used to assess the differences in annotations due to different software tools even when they start with the same transcript set for the basis of variant annotation. Please consult the README.md file, the paper cited above and its supplementary material for more details on the data and results obtained from it.