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How can I specify unmmaped regions with FastaAlternateReferenceMaker
I have a set of high-quality SNPs that were jointly called off a merged, realigned BAM. I then created a VCF for each sample using SelectVariants, re-ran UnifiedGenotyper with EMIT_ALL_SITES, and thinned the resulting VCF to no-call sites so I could mask them. Next, I produced a FASTA file for each sample with Ns at no-call sites and SNPs in their appropriate positions with FastaAlternateReferenceMaker. How can I use GATK to specify contigs where no reads were supported for a given sample and use this information to avoid outputting these regions via the -L flag with FastaAlternateReferenceMaker? Apologies if this is trivial, but I haven't found a clear solution.