Evaluating the quality of the 1000 genomes project data.

ABSTRACT:

Background

Data from the 1000 Genomes project is quite often used as a reference for human genomic analysis. However, its accuracy needs to be assessed to understand the quality of predictions made using this reference. We present here an assessment of the genotyping, phasing, and imputation accuracy data in the 1000 Genomes project. We compare the phased haplotype calls from the 1000 Genomes project to experimentally phased haplotypes for 28 of the same individuals sequenced using the 10X Genomics platform.

Results

We observe that phasing and imputation for rare variants are unreliable, which likely reflects the limited sample size of the 1000 Genomes project data. Further, it appears that using a population specific reference panel does not improve the accuracy of imputati

SUBMITTER: Belsare S 

PROVIDER: S-EPMC6696682 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature