- Cambridge, MA
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- Member, Administrator, Broadie
As you responded in an earlier message:
"Potentially, yes. If you have different expression of two alleles, and one is very low, you may not be able to call them correctly -- e.g. you may call the wrong genotype, or miss the call altogether (if it looks hom-ref).
I am calling variants with RNAseq data using gatk. Since the missing call for hom-ref (i.e. 0/0) may affect the calculation of heterozygosity of a population a lot, is it possible to recover 0/0? If not, how should I properly deal with loci with 0/0 so that the heterozygosity will not be biased?
In my vcf files from gatk, missing genotypes are represented in two ways, "./." and ".". Although documentations indicate that they represent diploid and haploid genotypes that are missing, it is still unclear why they are different. Could you please provide some hints on what may generate "./." and "."? Also, is "." actually hom-ref (i.e. 0/0)?