Dear GATK Team..,

I intend to mask variants that have low quality (DP less than 8) using Fasta Alternate Reference Maker. First, I select variant using SelectVariant with command below:

Low quality variant filtering (to be masked with NNNN in fasta alternate, GATK)

java -jar GenomeAnalysisTK.jar -T SelectVariants -R genome_dmir_rename.fasta -V ${acc}${strain}_realigned.vcf -o ${acc}${strain}_masked.vcf --select "DP<8"

Then I used the masked vcf into FastaAlternateReferenceMaker
java -jar GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R genome_dmir_rename.fasta -o ${acc}${strain}_realigned.fas -L posgen.bed -V ${acc}${strain}snp.vcf --snpmask ${acc}${strain}masked.vcf --use_IUPAC_sample ${acc}${strain}

I found many sites in masked vcf but in the fasta produced by Fasta Alternate, they were not reported as NNNN but as reference insted.

How can I solve this issue?

Any help will be much appreciated