liftover-coordinates

To convert genomic coordinates from hg19 to hg38, you input your source assembly coordinates and specify the target assembly. The Skill uses UCSC chain files and tools like CrossMap to ensure accurate position mapping across different genome assemblies.

Yes, you can use CrossMap to liftover VCF and BED files between genome assemblies. The Skill handles multiple formats including BED, VCF, bigWig, and BAM, ensuring accurate conversion across multiple species and versions.

The best way to track provenance during a genome coordinate liftover is by logging conversion details automatically. This Skill records chain files, tools used, and loss rates to ensure your bioinformatics workflow remains fully reproducible.

Yes, this genomic coordinate conversion handles unmapped regions in GWAS data. When combining datasets like hg19 GWAS data with GRCh38 ENCODE peaks, the Skill automates the liftover process and properly manages regions that fail to map.

You need UCSC chain files for genomic coordinate conversion because they provide the mapping matrix between different genome assemblies. The Skill relies on these chain files alongside tools like rtracklayer and the Ensembl REST API to ensure accurate results.

You should avoid using the Ensembl REST API for liftover coordinate conversion when working with large batch files like BAM or bigWig, as local tools such as CrossMap or UCSC liftOver paired with chain files offer better reproducibility and provenance tracking.