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GenotypeGVCFs liftOver problem?

Hi,
I am trying to run GenotypeGVCFs on my combined gvcf file 'cohort.g.vcf' and i am getting the following error:

A USER ERROR has occurred: Given reference file does not have data at the requested contig(ChroChromosome01)!

I don't understand why this is happening as i used the same reference genome for all previous steps (such as variant calling,CombineGVCFs). Do i need to liftOver genomic coordinates on the VCF file based on the reference genome? I am trying to use flo to get the chain file for my reference genome and then use that chain file as input to picard tool liftOverVCF or liftOvervariants?. I'm just not sure why i have to do this as the vcf should match the reference genome coordinates as i am using the same reference throughout. Please help

Answers

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