The creation of the GIAB Problematic Regions tracks involves using a pipeline and configuration to generate stratification BED files that categorize genomic regions based on specific challenges, such as low complexity or difficult mapping, to facilitate accurate benchmarking of variant calls. For more information on the pipeline and configuration used, please visit the following webpage: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/README.md.
++The raw data can be explored interactively with the +Table Browser or the +Data Integrator. The data can also be +accessed from scripts through our REST +API.
++This track is a container of multiple subtracks; the underlying data are stored in bigBed files +that can be downloaded from our +download server. +Individual regions or the whole genome annotation can be obtained using our tool +bigBedToBed, which can be compiled from the source code or downloaded as a precompiled +binary for your system. Instructions for downloading source code and binaries can be found +here. +The tool can also be used to obtain only features within a given range, for example:
+bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/problematic/GIAB/alldifficultregions.bb -chrom=chr6 -start=0 -end=1000000 stdout ++Please refer to our +mailing +list archives for questions, or our +Data Access FAQ for more +information.
+If you have questions or comments, please write to Justin Zook (jzook@nist.gov).
Dwarshuis N, Kalra D, McDaniel J, Sanio P, Alvarez Jerez P, Jadhav B, Huang WE, Mondal R, Busby B, Olson ND et al. The GIAB genomic stratifications resource for human reference genomes. Nat Commun. 2024 Oct 19;15(1):9029. PMID: 39424793; PMC: PMC11489684
Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA,