BED files are plain text, tab-delimited files which list genomic coordinates. These files may be used to explore design targets and to assess capture performance within the targeted regions. The first 3 columns are chromosome or sequence name, target start (0-based), and target end (1-based). For selected SeqCap EZ designs, the fourth column of primary and capture target BED files shows associated gene annotation for each genomic region.
BED files can be imported into Microsoft Excel as tab-delimited text or visualized using the SignalMap software.
The following files are included in the downloadable zip file:
- HGSC_VCRome_v2.1_hg18_primary_targets.bed: This file contains the design primary target (unpadded) in hg18 coordinates. Gene annotation is not provided.
- HGSC_VCRome_v2.1_hg18_capture_targets.bed: This file contains coordinates showing the probe footprint with no padding in hg18 coordinates.
- HGSC_VCRome_v2.1_hg18_coverage_summary.txt: This file describes the primary target size, the percentage of primary target bases directly covered by one or more probes (“Probe_Coverage”), and the percentage of primary target bases with estimated sequencing coverage for typical results (“Estimated_Coverage”). This file is only provided based on hg18 coordinates.
- HGSC_VCRome_v2.1_hg19_primary_targets.bed: This file contains the design primary target (unpadded) in hg19 coordinates and gene annotation in the 4th column.
- HGSC_VCRome_v2.1_hg19_capture_targets.bed: This file contains coordinates showing the probe footprint with no padding in hg19 coordinates.
- HGSC_VCRome_v2.1_hg19_UCSCBrowser.bed: This file is for viewing target coordinates in the UCSC Genome Browser. This file is only provided based on hg19 coordinates.
- HGSC_VCRome_v2.1_hg19_gene_list.txt: This file contains a list of gene names and symbols from multiple annotation sources (see file header). This file is only provided based on hg19 coordinates.