Hi,
I am running the following command in Linux for variant filteration:
gatk VariantFiltration -R hg19.fa -V NA12878.gatk.raw.vcf -O NA12878.gatk.raw.flag.vcf -filter “DP < 10.0” --filter-name “LowDP” -filter “QD < 2.0” --filter-name “QD” -filter “MQ < 40.0” --filter-name “MQD” -filter “FS > 60.0” --filter-name “FSsnp” -filter “FS > 200.0” --filter-name “FSindel”
I'm getting the below error for that command:
14:51:41.836 WARN JexlEngine - ![0,2]: 'DP < 10.0;' undefined variable DP 14:51:44.273 WARN JexlEngine - ![0,2]: 'DP < 10.0;' undefined variable DP 14:51:44.569 WARN JexlEngine - ![0,2]: 'DP < 10.0;' undefined variable DP 14:51:45.322 INFO ProgressMeter - chr11:67440041 0.2 362000 2169830.2 14:51:46.801 WARN JexlEngine - ![0,2]: 'DP < 10.0;' undefined variable DP 14:51:48.077 WARN JexlEngine - ![0,2]: 'DP < 10.0;' undefined variable DP 14:51:49.353 WARN JexlEngine - ![0,2]: 'DP < 10.0;' undefined variable DP
The command also generating the output file (filtered vcf file), but has the same number of variants in the input file.
I really don't know what is going wrong. Is that correct syntax for that command? Can anyone of you help me out ?
Thanks in advance!