variantFiltration error

[elbakrifz]

I was running the following command line : java -Xmx8G -jar /Users/mac/Downloads/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar -VariantFiltration \ -R /Users/mac/Desktop/LmjFwholegenome_20070731_V5.2.fasta \ -V /Users/mac/Desktop/NGS-/57variants.vcf \ --filterExpression "QD < 2.0 || MQ < 50" -filterName "hard_filtering_snp" / -o /Users/mac/Desktop/NGS-/59varians_filt.vcf
I get :
A USER ERROR has occurred: '-VariantFiltration' is not a valid command.
Did you mean this?
VariantFiltration

---

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

[yunfeiguo]

Hi @elbakrifz
It should be used with -T option, e.g. -T VariantFiltration.

[elbakrifz]

when I used, I get A USER ERROR has occurred: ' -T' is not a valid command

[yunfeiguo]

Maybe you should follow gatk doc since you are gatk4? https://gatk.broadinstitute.org/hc/en-us/articles/360037269391-VariantFiltration

[elbakrifz]

the following CML didn't have "-T"
gatk VariantFiltration
-R reference.fasta
-V input.vcf.gz
-O output.vcf.gz
--filterExpression "AB < 0.2 || MQ0 > 50"
--filterName "my_filters"
how should I fix it ??!

[yunfeiguo]

Sorry I cannot help. Please post this question GATK help forum (they are GATK experts).