How to filter GATK vcf file using other programs

Question

[reza]

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

[Pierre Lindenbaum]

what is the full stacktrace ? find the value 10.09 in the vcf . What is the corresponding INFO definition ? is it defined as an Integer. see also: https://gatk.broadinstitute.org/hc/en-us/community/posts/360072157591-NumberFormatException-Error-in-VariantFiltration ; https://gatk.broadinstitute.org/hc/en-us/community/posts/360072140012-Variant-Filtration-error-Number-format-exception-

[reza]

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.

[Pierre Lindenbaum]

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

[reza]

My-hp:~$ echo ${LANG}

en_US.UTF-8