The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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”