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--snpmask in FastaAlternateReferenceMaker not inserting N?
(PS I've posted this as a comment under another thread, but figured that the title of that other thread might be too obscure)
I read a few other posts regarding FastaAlternateReferenceMaker with snpmask. Here's how I constructed mine to mask sites (for one particular sample, just to test) that have low quality (DP below 8). I first emit all site (BP_RESOLUTION) under HC fand then use -allSites under GenotypeGVCFs. From this all-sites VCF, I then used SelectVariants to select sites that have DP < 8 under INFO. This presumably gives me a vcf-formated masking file for use in the final step. However, after I have run FastaAlternateReferenceMaker with this file and --snpmask, masked sites are still showing reference nucleotide, instead of N. Here's my last command:
java -jar GenomeAnalysisTK.jar \
-T FastaAlternateReferenceMaker \
-R arach.uce.mar17.cs.fa \
-o Al_12620.alt.ref.fasta \
-V Al_12620.allsites.vcf \
--snpmask mask.vcf \
What is it that I'm doing wrong here? I'm running version 3.3.