Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Could anyone help me with this error?
liftOverVCF.pl \ -vcf NA12878.genotypes_chr1_CEU_r28_nr.b36_fwd.GenomeWideSNP_6.vcf \ -chain $dbDir/b36tob37.chain \ -out NA12878.genotypes_chr1_CEU_r28_nr.b37_fwd.GenomeWideSNP_6.vcf \ -gatk GATK-2.8-1 \ -newRef broad_bundle_b37_v2.8/human_g1k_v37.fasta \ -oldRef iGenome/Homo_sapiens/NCBI/build36.3/Sequence/WholeGenomeFasta/genome.fa
The chain file is from https://github.com/broadgsa/gatk/tree/master/public/chainFiles
The error I got is this:
“##### ERROR MESSAGE: 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”