Does anyone know if it is possible to convert SNP coordinated from Hapmap database to the new reference genome. UCSC doesn't have the liftover yet ready. Any suggestions?
try NCBI remap: https://www.ncbi.nlm.nih.gov/genome/tools/remap
NCBI's remap is a great alternative to liftOver, and a standalone script can be found here. It doesn't accept HapMap's old format, but will take VCFs. At this FTP link, Ensembl lists HapMap variants in VCFs mapped to GRCh37.p13. And remap-ing GRCh37.p13 to GRCh38 should cause fewer conflicts than hg18 to GRCh38. In the remap tool, be sure to set the Source Assembly to GRCh37.p13 instead of GRCh37.
An hg18ToHg38 chain file is now available for liftOver. But since you're interested in HapMap variants, it is best to start with the GRCh37.p13 VCFs from Ensembl. And then liftOver those VCFs to GRCh38 using the hg19ToHg38 chain file. If you have trouble with UCSC's different chromosome names, use NCBI's remap instead, and map GRCh37.p13 to GRCh38.
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cross-posted http://stackoverflow.com/questions/21913057
There's a pretty comprehensive post on this topic here: Converting genome coordinates from one genome version to another (UCSC liftOver, NCBI Remap, Ensembl API)