Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2024 Jan 23;40(2):btae038. doi: 10.1093/bioinformatics/btae038

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2024. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

PMC Copyright notice

Figure 6. — Examples of different liftover scenarios with discordance between BCFtools/liftover and either Transanno/liftvcf (a, b) or Genozip/DVCF (c, d) where the latter tools are unable to recognize the need for a swap of the reference with the alternate allele in the indel record. In each scenario, the 3’ anchor fails to map to the new assembly due to a small gap in the chain outlining the alignment between the two assemblies. BCFtools/liftover uses the Needleman-Wunsh algorithm to realign the sequence overlapping the gap and assess which base pair in the new assembly should act as a 3’ anchor. Underlined base pairs are base pairs covered by the hg19ToHg38.over.chain.gz chain file. Gray base pairs are 5’ and 3’ anchors for the maximally extended representations of the records.