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Issues in Filtering by AF
I have used the GATK pipeline and generated vcf files after using Haplotypecaller, GenomicsDBImport and GenotypeGVCFs.
I am working with a non model organism and I am currently filtering the variants.
This is my JEXL for VariantFiltration:
"QD < 2.0 || FS > 60.0 || MQ < 50.0 || MQRankSum < -2.0 || ReadPosRankSum < -2.0 || AF < 0.01"
Everything is fine with this expression except that a few very low AF values have been recorded as power by GenotypeGVCFS in the final vcf.
For example: AF=1.094e-03 which is the result of 1/914, and needs to be filtered out as it is well below 0.01.
These AF are not filtered out by my expression and I am trying to find an alternative way to remove them. Any suggestion?