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How to produce GVCF files that were produced from a different reference genome?
Hi everyone. I have got my genotyped vcf file successful produced but I needed to merge them with other g.vcf files I recently received from a collaborating company. These were gzipped vcf files with their associated .tbi files. I had to first unzipped them in order to combining them by using GenotypeGVCF tool to create a genotype vcf file. It appeared that these files had different contigs names from reference genome (g.vcf contig names as 1,2,3, whereas my reference contig naming is chr 1, ..). Luck enough I were able to rename the contig names to match the reference contig names, however, the merging process by using GenotypeGVCF still didn't work out. This time the error was regarding that these g.vcf files contigs were not in the same order to that of my reference. However, in attempt of reordering the contig names to match the ordering in the reference using sortVCF in picard tools, I receieved error information that I really couldn't be able to solve. Could anyone kindly help me out? Please find the attachment of the various stages and error information.