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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?


Best Answer


  • 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?

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