Convert genome coordinates between assemblies
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Docker image for CrossMap.
Convert genome coordinates between assemblies.
CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome.
It includes the following chain files (in /chain_files/human/ directory):
GRCh37_to_GRCh38.chain.gz
GRCh37_to_NCBI34.chain.gz
GRCh37_to_NCBI35.chain.gz
GRCh37_to_NCBI36.chain.gz
GRCh38_to_GRCh37.chain.gz
GRCh38_to_NCBI34.chain.gz
GRCh38_to_NCBI35.chain.gz
GRCh38_to_NCBI36.chain.gz
NCBI34_to_GRCh37.chain.gz
NCBI34_to_GRCh38.chain.gz
NCBI35_to_GRCh37.chain.gz
NCBI35_to_GRCh38.chain.gz
NCBI36_to_GRCh37.chain.gz
NCBI36_to_GRCh38.chain.gz
Docker file here.
Content type
Image
Digest
Size
283.5 MB
Last updated
over 6 years ago
docker pull miguelpmachado/crossmap:0.3.9