Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

Conversion of vcf to gvcf

I am trying to combine and convert two VCF 4.1 files (an SNP VCF and an INDEL VCF) to VCF 4.2 (which, if I understood correctly is the same thing as gVCF). The resulting file would then be used as input to a third-party analysis software. The files are based on the GRCh37 reference genome.

However, despite searching the forum, I was unable to find a solution that would directly combine and convert both files into gVCF. Therefore, one possibility would be to first merge the two files with CombineVariants, second, convert the resulting file to a BAM file through SimulateReadsForVariants and, third, to derive the gVCF file through HaplotypeCaller.

Would this approach work or would you rather suggest a different and maybe simpler approach?

Thanks

Best Answer

Answers

  • A vcf and g.vcf contain different kinds of information, VCF 4.2 is just the version of the standard. It makes no sense to 'convert' between vcf and g.vcf, in the same way that you don't convert a .bam file to a .vcf file. See https://gatkforums.broadinstitute.org/gatk/discussion/4017/what-is-a-gvcf-and-how-is-it-different-from-a-regular-vcf for details on the difference between vcf and g.vcf.

  • Thanks for the reply and for the link!

    I understand that this type of conversion is not usually done, but I need to have my data in a format that is compatible with the third-party tool I am planning to use, plus I need all my data in a single file (the tool only takes one file). Can you expand on your comment that it makes no sense to do the conversion? E.g. will 3 step conversion scheme described above not work or is it simply bad form?

Sign In or Register to comment.