Lifting over my positions¶
This stage is optional, and will be performed only if an input file is specified with --annotation, together with its file type using --annotation_format:
nextflow run evotools/nf-LO --source GRCh37 --target GRCh38 --aligner minimap2 --distance near --annotation s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf --annotation_type gff
Algorithms¶
The lift over can be performed in two different ways:
Using the UCSC liftOver algorithm (
--liftover_algorithm 'liftover')Using the crossmap software (
--liftover_algorithm 'crossmap')
Keep in mind that, if the file type is different from bed and gff, crossmap will be used by default since liftOver cannot accept these files:
File type |
Software used |
|---|---|
gtf/gff |
liftOver/crossmap |
bed |
liftOver/crossmap |
vcf |
crossmap |
bam |
crossmap |
maf |
crossmap |