Finding easy regions for short-read variant calling from pangenome data.

ABSTRACT:

Background

While benchmarks on short-read variant calling suggest a low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher. Although multiple sets of easy regions have been identified to alleviate the issue, they fail to consider nonreference samples or are biased toward existing short-read data or aligners.

Results

Here, using hundreds of high-quality human assemblies, we derived a set of sample-agnostic easy regions where short-read variant calling reaches high accuracy. These regions cover 88.2% of GRCh38, 92.2% of coding regions, and 96.3% of ClinVar pathogenic variants. They achieve a good balance between coverage and easiness and can be generated for other hum

SUBMITTER: Li H 

PROVIDER: S-EPMC12409275 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature