How can an individual in a vcf file have one called and one missing allele? I generated a dataset in GATK and did not encounter this in my GATK generated vcfs. However in comparative data vcfs I saw this. But I dont understand how this call is generated in a vcf file. I thought it was when the position had very low coverage, maybe one read only and then one allele can be called only. But some of the missing/allele calls had high read depth. Some more info: It is a single individual vcf and a low percentage of sites (around 0.1%) had one called allele and one missing allele, for instance [0/.] or [1/.] . Could somebody explain what is the reason that such calls exist and is it advisable to filter these out of the data?
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