Year: 2024
Type: article
Abstract: Background: Liftover tools are one of the practical alternatives for genome conversion when realignment is not possible.However, these tools often cannot handle differences in alleles between assemblies in case of insertions/deletions (indels).Recently, BCFtools/liftover was developed to support the genome conversion of indels.As such, the aim of this study was to investigate the genome conversion of indels using BCFtools/liftover.Methods: Two variant call format (VCF) files aligned to GRCh37 and GRCh38 were downloaded from ClinVar (https://ftp.ncbi.nlm.nih.gov/pub/clinvar/).We used 23,419 ClinVar indels.BCFtools/liftover was used to convert genome coordinates from GRCh37 to GRCh38.The liftovered variants from GRCh37 to GRCh38 were compared with GRCh38-aligned variants.RepeatMasker track information from UCSC was used to determine whether the variants are located in repetitive sequence regions.Results: Compared with the GRCh38-aligned variants, eight variants (0.03%) were not detected among the variants converted with the BCFtools/liftover.The nomenclature of the 20 liftovered variants, including multiallele variants (N =19), did not agree with that of the GRCh38aligned variants.The tool successfully converted most of the indels located in repetitive sequence regions (99.82%).Conclusions: This study demonstrated the applicability of BCFtools/liftover for the genome conversion of indels.BCFtools/liftover can be used to accurately perform the genome conversion of indels located in repetitive sequence regions.BCFtools/liftover must be used cautiously when the indels are converted to multiallele variants.Further clinical studies are warranted to investigate the performance of BCFtools/liftover using a number of indels in a routine clinical setting.
Source: Laboratory Medicine Online
Authors: Kyoung-Jin Park, Jong-Ho Park, Eunkyoung You
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Award: G4167815677
OpenAlex ID: W4402886392