Hi!

I am using the snakemake to run the gatk pipeline, but when I run the VariantFiltration, I get the following error:

/bin/bash: -8.00: No such file or directory

My code looks like this:

rule gatk_VariantFiltrationSNP:
        input: rules.gatk_SelectVariantsSNP.output
        output: "out_VariantFiltration/{sample}.VariantFiltration_snp.vcf"
        shell: "./gatk-4.1.9.0/gatk --java-options ""-Xmx30g""  VariantFiltration -V {input}  --filter-name ""HDFLT_SOR3.00""  --filter-expression ""SOR > 3.00""  --filter-name ""HDFLT_ReadPosRankSum-8.00""  --filter-expression ""ReadPosRankSum < -8.00""  --filter-name ""HDFLT_MQRankSum-12.50""  --filter-expression ""MQRankSum < -12.50""  --filter-name ""HDFLT_QUAL30.00""  --filter-expression ""QUAL < 30.00""  --filter-name ""HDFLT_FS60.00""  --filter-expression ""FS > 60.00""  --filter-name ""HDFLT_MQ40.00""  --filter-expression ""MQ < 40.00""  --filter-name ""HDFLT_QD2.00""  --filter-expression ""QD < 2.00""  -O {output} "           

I don't understand what exactly the problem is. I would be grateful for any help!