How to filter GATK vcf file using other programs
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6 weeks ago
reza ▴ 270

hi everyone

I called variants for a WGS project using GATK (HaplotypeCaller). Now, when I want to filter that VCF file by VariantFiltration command in GATK, so the following error message appears.

java.lang.NumberFormatException: For input string: "10.90"

I asked my question in the GATK forum and unfortunately I did not get an answer.

it is worth mentioning that I get mentioned error in both GATK4 and GATK3.7.

  1. is there any way to fix this error?

  2. Can I do filter VCF file based on "QD < 2 || FS > 60 || MQ < 40 || MQRankSum < -12.5 || ReadPosRankSum < -8 || SOR > 3" criteria using other program like bcftools or vcftools

I will be very happy if you help me to solve this problem

Thanks

VCF Filtration GATK • 374 views
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this is my question link in GATK forum. 10.90 is related to QD and when I remove QD from the command, I get another error: 0.000 instead of 10.90.

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what is the output of echo ${LANG} ? Try to set the locale to english (well I think GATK should set it to english internally but it's worth trying)

export LANG=en_US.UTF-8
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My-hp:~$ echo ${LANG}

en_US.UTF-8
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