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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?