How to filter and annotate variants for influenza virus?

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8.5 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 • 2.2k views

ADD COMMENT • link updated 20 months ago by Ram 43k • written 8.5 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 4.4 years ago by Ram 43k • written 8.5 years ago by Pierre Lindenbaum 161k

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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 4.4 years ago by Ram 43k • written 8.5 years ago by bioinforesearchquestions ▴ 370

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ok, I didn't know that option.

ADD REPLY • link updated 4.4 years ago by Ram 43k • written 8.5 years ago by Pierre Lindenbaum 161k

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