I'm trying to filter a vcf file with SNPs using the following code:
java -jar GenomeAnalysisTK.jar \
-T VariantFiltration \
-R reference.fasta \
-V My_Snps.vcf \
--filterExpression "DP < 10 || DP > 300 " \
--filterName "Filter" \
-o My_filtered_Snps.vcf
But absolutely all lines in my output get a PASS. I've (1) visually inspected the file and I'm sure some lines must get the FILTER mark and (2) run an equivalent command in vcftools. The output has less lines than the original file. In other words, VariantFiltration is failing to get my lines right. Am I missing something in my code? (Outside the scope of the question: I could switch to another program, but I'd prefer to stick to GATK for several reason).
Thanks!