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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.

Comments

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @David_Mauki
    Hi,

    It looks like some VCFs are using hg19 (chr) and some are using b37 (without chr).

    You can use Picard's LiftoverVCF to liftover a VCF from one reference build to another. Please note, this is not the best way to go about this. The best thing to do is get the original BAM files, align all them all to the same reference, and do variant calling on them all together.

    -Sheila

  • Dear Sheila,

    Thank you so much for your solution. indeed this is what I also came to find out. With regard to the BAM files, is there any possible way to produce BAM files from these given g.vcf files? or rather should I have to ask for the original BAM files from the collaborating company?

    Regards
    David

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @David_Mauki
    Hi David,

    There is no way to produce BAM files from GVCF files. You will need to ask for the original BAM or FASTQ files. If you can get the original BAM files, you may find this article helpful.

    -Sheila

  • @ Sheila,

    I thank you.

    Regards
    David

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