This container track helps call out sections of the genome that often cause problems or confusion when working with the genome. The hg19 genome has a track with the same name, but with many more subtracks, as the GeT-RM and Genome-in-a-Bottle artifact variants do not exist yet for hg38, to our knowledge. If you are missing a track here that you know from hg19 and have an idea how to add it hg38, do not hesitate to contact us.

Problematic Regions

The Problematic Regions track contains the following subtracks:

• The UCSC Unusual Regions subtrack contains annotations collected at UCSC, put together from other tracks, our experiences and support email list requests over the years. For example, it contains the most well-known gene clusters (IGH, IGL, PAR1/2, TCRA, TCRB, etc) and annotations for the GRC fixed sequences, alternate haplotypes, unplaced contigs, pseudo-autosomal regions, and mitochondria. These loci can yield alignments with low-quality mapping scores and discordant read pairs, especially for short-read sequencing data. This data set was manually curated, based on the Genome Browser's assembly description, the FAQs about assembly, and the NCBI RefSeq "other" annotations track data.
• The ENCODE Blacklist subtrack contains a comprehensive set of regions which are troublesome for high-throughput Next-Generation Sequencing (NGS) aligners. These regions tend to have a very high ratio of multi-mapping to unique mapping reads and high variance in mappability due to repetitive elements such as satellite, centromeric and telomeric repeats.
• The GRC Exclusions subtrack contains a set of regions that have been flagged by the GRC to contain false duplications or contamination sequences. The GRC has now removed these sequences from the files that it uses to generate the reference assembly, however, removing the sequences from the GRCh38/hg38 assembly would trigger the next major release of the human assembly. In order to help users recognize these regions and avoid them in their analyses, the GRC have produced a masking file to be used as a companion to GRCh38, and the BED file is available from the GenBank FTP site.

Highly Reproducible Regions

The Highly Reproducible Regions track highlights regions and variants from eight samples that can be used to assess variant detection pipelines. The "Highly Reproducible Regions" subtrack comprises the intersection of the reproducible regions across all eight samples, while the "Variants" subtracks contain the reproducible variants from each assayed sample. Both tracks contain data from the following samples:

• a Chinese Quartet, samples CQ-5, CQ-6, CQ-7, CQ-8
• a HapMap Trio, samples NA10385, NA12248, NA12249
• a Genome in a Bottle sample, NA12878s

GIAB Problematic Regions

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.

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. If you have questions or comments, please write to Justin Zook (jzook@nist.gov).

To view the full description, click here.