How to filter GATK vcf file using other programs
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.
is there any way to fix this error?
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
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