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Can FastaAlternateReferenceMaker put Ns instead of the reference bases where there is no-call ?

Dear GATK team,

I'm using FastaAlternateReferenceMaker to generate a fasta file per sample. To do so, I had to first generate a vcf file per sample and use FastaAlternateReferenceMaker to generate a fasta file. Everything went well except that in any position where the genotype of a given sample was a no-call (./. or ./) it put the reference bases while I would prefer to have Ns instead.

I have looked over a similar post (https://gatkforums.broadinstitute.org/gatk/discussion/5778/can-fastaalternatereferencemaker-put-n-instead-the-reference-base-when-data-is-bad). It basically explained that we could use SelectVariants to select only sites with certain criteria and make a vcf that could be fed on FastaAlternateReferenceMaker via -snpmask. However, being no-call or not for a genotype is not a criteria we can use for SelectVariants.

So, how can I tell GATK to only select sites with no-call genotype ?

Answers

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