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Hi,
I have mapped reads with bwa against hg19, however the vcf file I have was created against hg18, So I need to create a lifted vcf that corresponds to hg19
when I run .
/liftOverVCF.pl -vcf ./SORTED_2010_07.vcf -chain ./hg18ToHg19.over.chain -out lifted.hg19.vcf -gatk /bin/GenomeAnalysisTK-1.6-5-g557da77 -newRef ./hg19.fa -oldRef ./hg18.fa
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
I have also tried the broad's chain file hg19toHg18.chain and b37tohg18.chain, same errors
Do I need to use the exact same hg18/19 fasta files that are at UCSC, ie including the *_random" and "chr*_ctg5_hap1" contigs. These are in the chain files. My 2 input files and vcf are sorted in karyotype order.
I have mapped reads with bwa against hg19, however the vcf file I have was created against hg18, So I need to create a lifted vcf that corresponds to hg19
when I run .
/liftOverVCF.pl -vcf ./SORTED_2010_07.vcf -chain ./hg18ToHg19.over.chain -out lifted.hg19.vcf -gatk /bin/GenomeAnalysisTK-1.6-5-g557da77 -newRef ./hg19.fa -oldRef ./hg18.fa
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
I have also tried the broad's chain file hg19toHg18.chain and b37tohg18.chain, same errors
Do I need to use the exact same hg18/19 fasta files that are at UCSC, ie including the *_random" and "chr*_ctg5_hap1" contigs. These are in the chain files. My 2 input files and vcf are sorted in karyotype order.
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