Description
The Genome in a Bottle (GIAB) Problematic Regions tracks provide stratifications of the
genome to evaluate variant calls in complex regions. It is designed for use with Global Alliance
for Genomic Health (GA4GH) benchmarking tools like
hap.py
and includes regions with low complexity, segmental duplications, functional regions,
and difficult-to-sequence areas. Developed in collaboration with GA4GH, the
Genome in a Bottle (GIAB) consortium, and the
Telomere-to-Telomere Consortium (T2T), the dataset aims to standardize the
analysis of genetic variation by offering pre-defined BED files for stratifying true and false
positives in genomic studies, facilitating accurate assessments in complex areas of the genome.
Methods
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.
Data Access
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/hs1/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.
Contact
If you have questions or comments, please write to Justin Zook (jzook@nist.gov).
References
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,
Tezak Z, Lababidi S
et al.
Best practices for benchmarking germline small-variant calls in human genomes.
Nat Biotechnol. 2019 May;37(5):555-560.
PMID:
30858580; PMC:
PMC6699627