I'm working on a project in which I'd like to annotate a VCF with features from the ExAC database. The VCF was generated with GATK against the hg19 reference, with naming conventions chr1 chr2 ... etc. The ExAC database uses GRCh37/hg19 (http://exac.broadinstitute.org/faq), however, it follows the naming convention 1, 2 ... etc which suggests b37. But the link off the ExAC site goes to a broad address with the file Homo_sapiens_assembly19.fasta.
When I try to do a liftover with the GATK LiftoverVariants tool with b37tohg19.chain I get the error
"Bad input: the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference"
The ExAC data only contains variants for 1-22, X and Y. Can I simply rename the chromosomes to chr1 etc and count on hg19 == hg19? Any suggestions on how to verify that the ExAC reference genome == the Broad GATK resource pack hg19 genome?
Thanks
Alex
When I try to do a liftover with the GATK LiftoverVariants tool with b37tohg19.chain I get the error
"Bad input: the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference"
The ExAC data only contains variants for 1-22, X and Y. Can I simply rename the chromosomes to chr1 etc and count on hg19 == hg19? Any suggestions on how to verify that the ExAC reference genome == the Broad GATK resource pack hg19 genome?
Thanks
Alex
Comment