How to use the the filters created from VariantFiltration while using Annovar?

Question

[deepue]

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 Annovar? I couldn't find any filter parameters in the Annovar commands.

Thanks

Answer 1

[Sean Davis]

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?

[deepue]

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

[Sean Davis]

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

• http://vcftools.sourceforge.net/man_latest.html#SITE%20FILTERING%20OPTIONS
• http://snpeff.sourceforge.net/SnpSift.html#filter

[deepue]

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

[Sean Davis]

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.