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SelectVariants on AF
I'm trying to do what I think should be pretty straightforward, which is to select sites in a VCF (generated by GATK) where the AF > 0.1. I have in my SelectVariants statement:
java -jar -Xmx8g /path/to/gatk-3.3-0/GenomeAnalysisTK.jar -T SelectVariants \
-R /path/to/ref/ref.fa \
-V /path/to/vcf/variants.vcf \
-select "AF > 0.1" \
However I get the following message:
Invalid JEXL expression detected for select-0 with message ![0,8]: 'AF > 0.1;' > error
I'm wondering if the reason for this is because in my VCF there are some sites with multiple alleles (and hence multiple AFs) and is therefore an array? This is from my VCF header:
INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
If this is the case, what would be the syntax to get GATK to look at the whole array of AFs? Or do I have to get rid of the multi-alleleic sites from my VCF? Or maybe I'm misinterpreting the error message?