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In trying to use VariantFiltration to hard filter vcf I continue to get the same runtime warning, e.g.
WARN 15:28:05,017 Interpreter - ![0,2]: 'DP;' undefined variable DP
and all sites have 'FILTER' set to 'PASS'.
Here a typical command:
java -jar /software/gatk/3.4-46/static/GenomeAnalysisTK.jar \
-T VariantFiltration \
-L 3R:12000000-12200000 \
-R /home/chuck/shrd/reference_genomes/D_mel_RELEASE6_Sue/norm_dmel_R6_SL.fasta \
-V /home/chuck/chl_working/testgatk/DPGP3_ZI118N.raw.snps.indels.gGVCF.g.vcf \
--filterName test_DPGT38 \
--filterExpression "DP>38.0" \
I suspect I am missing an obvious requirement or constraint.
Any help appreciated.