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Unable to filter VCF file using VariantFiltration for GATK 3.7.0

bhidebhide Purdue UniversityMember
I have couple of questions

1) I am using GATK 3.7 version for VariantFiltration step. I have generated vcf file using HaplotypeCaller, run GenotypeGVCF
followed by SNP and indel recalibration, snpEff and VariantAnnotator before running this VariantFiltration step.

All the steps have been run using GATK 3.7.0 version.

It gives me following error when I try to run this command
GenomeAnalysisTK -T VariantFiltration \
-R genome.fasta \
-V input.ann.vcf \
--filterExpression "GQ < 20.0" --filterName "GQ" \
--filterExpression "VQSLOD <= 0" --filterName "VQSLOD" \
-o trial.vcf \

Error:
##### ERROR MESSAGE: Invalid argument value '<' at position 8.
##### ERROR Invalid argument value '20.0' at position 9.
##### ERROR Invalid argument value '<=' at position 16.
##### ERROR Invalid argument value '0' at position 17.

Secondly I would like to filter variants in Subtelomeric regions based on intervals file as follows
Chr1 1 27336 SubtelomericRepeat
Chr1 27337 92900 SubtelomericHypervariable
Chr1 92901 457931 Core
Chr1 457932 460311 Centromere
Chr1 460312 575900 Core

Please

Answers

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