Question: How to use the the filters created from VariantFiltration while using Annovar?
1
gravatar for deepue
4.1 years ago by
deepue110
Finland
deepue110 wrote:

Hi,

I have a vcf file with the variants flagged(PASS or FilterName) using VariantFiltration walker in GATK for an exome sample.

How to use the filter for annotating using the Annovar ? I couldn't find any filter parameters in the Annovar commands.

Thanks.

ADD COMMENTlink modified 4.1 years ago by Sean Davis25k • written 4.1 years ago by deepue110
0
gravatar for Sean Davis
4.1 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

You can simply apply Annovar to the filtered VCF or apply VariantFiltration to an Annovar-annotated VCF.  There is no need for Annovar to have filter parameters.  Or perhaps I misunderstood your question?

ADD COMMENTlink written 4.1 years ago by Sean Davis25k

Hi Sean,

I have a filtered VCF(VariantFiltration used) and have applied Annovar for it. 

There are same number of variants in the vcf file before and after filtration as the VariantFiltration only flags the variant record as PASS or filterName. How to identify these records in Annovar output ? How to remove them from annotation ? Any other suggestions in understanding them ?

Thanks

ADD REPLYlink written 4.1 years ago by deepue110
1

You can use vcftools, snpSift, or many other tools for filtering VCF files.  

http://vcftools.sourceforge.net/man_latest.html#SITE FILTERING OPTIONS

http://snpeff.sourceforge.net/SnpSift.html#filter

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Sean Davis25k

Hi Sean,

Thank you for the suggestions on how to filter the VCF files.

So, Annovar annotates the entire VCF file without considering the Filter values created by VariantFiltration  walker in GATK ? What might be the potential use of the filters created by VariantFiltration ?

Thanks

ADD REPLYlink written 4.1 years ago by deepue110

The uses of the filters created by VariantFiltration are left to you, the user.  If you (or the software you use) don't have a use for them, then there is no need to generate them.  

ADD REPLYlink written 4.1 years ago by Sean Davis25k
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