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Hi, I'm calling Variants with HaplotypeCaller in a population of 2 Parents and 7 F1-individuals. After read backed phasing I'm combining the vcf files of my genotypes with CombineVariants. In the outfile I very often find "./.". I thought this means there is no coverage at a certain position. But at many positions I do have good coverage. Why do I then get ./.? Moreover I used FastaAlternateReferenceMaker and created a new reference sequence including the variants from the parents. In that case, after I run HC and do the phasing and combine variants steps, I only get "./." at positions where there is really no coverage (as I can see in my mappings). Nadia

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Hi GATK team,

I have a VCF file (from GATK) containing variants for a total of 20 individuals and I'm wondering how to get the consensus sequences for each individual regarding its own polymorphism. Some individuals may not show polymorphism at a particular position in a contig whereas some others may. I've checked the GATK dedicated tool (FastaAlternateReferenceMaker) but it doesn't answer my question as only one consensus is generated. My requirement would be to get as many outputs files (containing consensus file) as mapped individuals.

Is there anyway to get this task achieved using GATK?

Thanks, C.