Question: how to add QualityOfDepth(QD) annotation to freebayes vcf
1
gravatar for William
5.5 years ago by
William4.7k
Europe
William4.7k wrote:

Is there a tool already out there that can add the QualityOfDepth(QD) annotation to a VCF file created by freebayes?

The general idea of variant QualityByDepth(QD) is explained here

https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_QualByDepth.php

and the detailed formula is the best answer (highlighted in green) here

http://gatkforums.broadinstitute.org/discussion/comment/18866

Freebayes outputs somewhat different fields than GATK. Instead of AC (allele count) per genotype:

##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">

##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">

The basic QD formula should be something like.

QD = QUAL / Sum (Sum (RO+AO)) (over just the samples that have a read that contributes to the variant call).

 

freebayes qualitybydepth vcf • 2.0k views
ADD COMMENTlink modified 5.4 years ago by Sean Davis26k • written 5.5 years ago by William4.7k
0
gravatar for Sean Davis
5.4 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

I believe GATK Variant Annotator

https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator.php

will do that for you.

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Sean Davis26k
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