GATK VariantFiltration error "-12.5 is not a recognized option"

Question

[chloe.girard]

Dear all,

I'm going nuts. It's been two days and I can't find what I'm doing wrong. I am trying to filter variants from a VCF files generated through HaplotypeCaller (output: gvcf) and then GenotypeGVCF (output: vcf), using GATK v4.1.9.0.

Then I want to perform hard filtering on my variants, using either SelectVariant or VariantFiltering. In all cases I want MQRankSum to be < -12.5

gatk VariantFiltration \
   -R  ~/Genomes/TAIR10_chr_all.fasta \
   -V ~/RIL_seq/$sample1.vcf.gz \
   -O ~/RIL_seq/$sample1$addon.vcf.gz \
   --filter-expression "QD < 2" \
   --filter-expression "FS > 60" \
   --filter-expression "MQ < 40" \
   --filter-expression "MQRankSum < -12.5" \
   --filter-expression "ReadPostRankSum < -8" \
   --filter-expression "GT == 0/1"

Same happens with

gatk SelectVariants \
   -R  ~/Genomes/TAIR10_chr_all.fasta \
   -V ~/RIL_seq/$sample1.vcf.gz \
   -I ~/RIL_seq/$sample1.bam \
   -O ~/RIL_seq/$sample1$addon1.vcf.gz \
   -select "GT == 0/1 || QD < 2 || FS > 60 || MQ < 40 || MQRankSum < -12.5 || ReadPostRankSum < -8" \
   --exclude-filtered true

Both times I get the error message:

A USER ERROR has occurred: -12.5 is not a recognized option

Thanks for your help, Best Chloé

[chloe.girard]

Hello all, I tried to put 0 as a value to bypass the problem

gatk VariantFiltration \
    -V ~/RIL_seq/$sample1.vcf.gz \
    -filter "QD < 2.0" --filter-name "QD2" \
    -filter "QUAL < 30.0" --filter-name "QUAL30" \
    -filter "SOR > 3.0" --filter-name "SOR3" \
    -filter "FS > 60.0" --filter-name "FS60" \
    -filter "MQ < 40.0" --filter-name "MQ40" \
    -filter "MQRankSum < 0" --filter-name "MQRankSum0" \
    -filter "ReadPosRankSum < 0" --filter-name "ReadPosRankSum0" \
    -O ~/RIL_seq/$sample1$addon4.vcf.gz

And now the error is :

A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',<{2.0{<{30.0{>{3.0{>{60.0{<{40.0{<{0{<{0}' but no positional argument is defined for this tool.

I am at a loss to explain this error message. Thanks for your help

[Pierre Lindenbaum]

replace gatk VariantFiltration with echo gatk VariantFiltration and show us the output. I f you hany space in those shell variables it will mess-up the command. Furthermore, protect your argument by quoting them.

not:

-V ~/RIL_seq/$sample1.vcf.gz \

but

-V "${HOME}/RIL_seq/$sample1.vcf.gz" \

[chloe.girard]

Hello Pierre, Thanks for your reply and sorry about the delay. I checked for typos and extra spaces, doesn't seem to be any (my terminal highlights extra spaces)

Following some rules from GATK website, my code now reads

export WRKPATH=/home/cg
export BINPATH=$WKRPATH/bin
export JOBPATH=$WRKPATH/RIL_seq
cd $JOBPATH

### Name variables
sample1=7R
addon1=_recalibrated
addon2=_filtered

/opt/singularity/calls_gatk/gatk VariantFiltration \
   -R "$WRKPATH/Genomes/TAIR10_chr_all.fasta" \
   -V "$JOBPATH/$sample1$addon1.vcf.gz" \
   -O "$JOBPATH/$sample1$addon1$addon2.vcf.gz" \
   --filter-name "QD2" \
   --filter-expression "QD < 2.0" \
   --filter-name "QUAL30" \
   --filter-expression "QUAL < 30.0" \
   --filter-name "SOR3" \
   --filter-expression "SOR > 3.0" \
   --filter-name "FS60" \
   --filter-expression "FS > 60.0" \
   --filter-name "MQ40" \
   --filter-expression "MQ < 40.0" \
   --filter-name "MQRS-12.5" \
   --filter-expression "MQRankSum < 0" \
   --filter-name "RPRS-8" \
   --filter-expression "ReadPosRankSum < 0"\
   --genotype-filter-name "HOM" \
   --genotype-filter-expression "isHomVar==1" \
   --genotype-filter-name "HET" \
   --genotype-filter-expression "isHet==1"

And I still get the same error!

A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',<{2.0{<{30.0??{>{3.0{>{60.0{<{40.0{<{0{<{0}' but no positional argument is defined for this tool.

As for the echo

echo /opt/singularity/calls_gatk/gatk VariantFiltration

only returns:

/opt/singularity/calls_gatk/gatk VariantFiltration