Conversion of gff3 to vcf4.2 file
Hi , I am trying to convert a gff3 file obtained using pbalign and variantCaller from SMRT tools 7.0 to a vcf4.2 file that I will be using with the R vcfR package. I tried gffToVcf but that does not yield the desired VCF file, since the VCF file produced has no genotype information, in fact the VCF file is missing the FORMAT column. How do I produce a VCF file that is suitable for the vcfR package ? Thanks, Ambarish.
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