How to filter and annotate variants for influenza virus?

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9.2 years ago

bioinforesearchquestions ▴ 370

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 • 2.3k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 9.2 years ago by bioinforesearchquestions ▴ 370

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

ADD REPLY • link updated 5.1 years ago by Ram 44k • written 9.2 years ago by Pierre Lindenbaum 164k

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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.

ADD REPLY • link updated 5.1 years ago by Ram 44k • written 9.2 years ago by bioinforesearchquestions ▴ 370

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ok, I didn't know that option.

ADD REPLY • link updated 5.1 years ago by Ram 44k • written 9.2 years ago by Pierre Lindenbaum 164k

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