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How to filter and annotate variants for influenza virus?

Hi All,

I have a vcf file from GATK tool. I would like to filter and annotate the variants. Can any one suggest some tutorials or links which explain the parameters for filtering. Also I am looking for some and for annotating and filtering the variants.

vcf gatk snp
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updated by Ram Ram • written by bioinforesearchquestions bioinforesearchquestions

as far as I know, GATK is only designed for diploid organisms...

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

I am using GATK's unified genotyper to call variants. I am using a haploid organism, and used the -ploidy flag to indicate that to unified genotyper.

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updated by Ram Ram • written by bioinforesearchquestions bioinforesearchquestions

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