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How to mark specific individual genotype as No Call
I have been trying to find a way to mark specific individual genotypes as No Call.
I know that in VariantFiltration it is possible to add the option --setFilteredGTToNocall in order to mark filtered genotypes as no call. However, in my case, there is no available filter corresponding to my criteria. Let me explain. I have some diploid-haploid paired related samples, i.e. I expect the haploid individual to share one of the two alleles from its diploid related. Therefore, for positions where there are discordant genotypes, I would like to mark individual genotypes as as no call in order to not include potentials errors in my data. I couldn't find a way to apply this rational to the pipeline of VariantFiltration or SelectVariants...
Eventually, I manage to manipulate the .vcf file by myself to mark any discordant genotypes as . or ./. However, when later I want to select the positions for which there are maximum of 0.2 ratio of no call (using the option --maxNOCALLfraction of SelectVariants from the nightly build version), there was an error message "there aren't enough comumns for line...". I suppose that it's because I did manipulate the vcf file by myself and there could have been errors (although I'm quite confident with my script).
Therefore, I think it's better to not manipulate the vcf file and try to do things using the pipeline....but how?