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lawal

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lawal
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  • Hi guys,
    I was trying to run the below command and I got an invalid error from my argument. I could not find any mistake in my command and have also regenerated my input raw SNPs file but error remain the same. I could not also find any thread that have addressed this problem. What do you think I am doing wrong?

    logfile=filtered.error
    gatk 3.7.0 \
    -T VariantFiltration \
    -R fasta.fa \
    -V raw_SNPs.vcf.gz \
    --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" \
    --filterName "default_SNP_filter" \
    -o filtered_SNPs.vcf \
    2> >(tee "$logfile")

    ERROR Invalid argument value '2.0' at position 9.
    ERROR Invalid argument value '||' at position 10.
    ERROR Invalid argument value 'FS' at position 11.
    ERROR Invalid argument value '>' at position 12.
    ERROR Invalid argument value '60.0' at position 13.
    ERROR Invalid argument value '||' at position 14.

    etc...

    December 2017