search

WGLab / SeqMule

Automated human exome/genome variants detection from FASTQ files
http://seqmule.usc.edu
Other
22 stars 22 forks source link

variantFiltration error #182

Open elbakrifz opened 3 years ago

elbakrifz commented 3 years ago

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 commented 3 years ago

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

elbakrifz commented 3 years ago

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

yunfeiguo commented 3 years ago

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

elbakrifz commented 3 years ago

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 commented 3 years ago

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