Question: How to filter and annotate variants for influenza virus?
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gravatar for bioinforesearchquestions
5.2 years ago by
United States
bioinforesearchquestions280 wrote:

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.

variants snp tools gatk vcf • 1.5k views
ADD COMMENTlink written 5.2 years ago by bioinforesearchquestions280

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

ADD REPLYlink modified 14 months ago by _r_am32k • written 5.2 years ago by Pierre Lindenbaum133k

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 REPLYlink modified 14 months ago by _r_am32k • written 5.2 years ago by bioinforesearchquestions280

ok, I didn't know that option.

ADD REPLYlink modified 14 months ago by _r_am32k • written 5.2 years ago by Pierre Lindenbaum133k
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