Question related to choosing GATK parameter for variant calling

[kjaja]

I am looking to call my samples that were exome sequenced using UnifiedGenotyper program within GATK. An example of a generic command is given in the following link under “Example generic command for multi-sample SNP calling” and I am assuming that it should work for calling a single sample

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html

I have a question on the –dcov option, what does it mean?
Also, I have seen examples of where they added -A DepthOfCoverage \
-A AlleleBalance \. Is there an optimal parameter setting to call variants for exome sequencing?

Thanks,

[vdauwera]

You should look up the meaning of these arguments in the technical documentation for GATK. For example, you can find the description of -dcov here: http://www.broadinstitute.org/gatk/g...dLineGATK.html

For more information on downsampling (which is what -dcov controls), see this article:

http://www.broadinstitute.org/gatk/guide/article?id=1991

The annotation parameters (set using the -A flags) have no effect on the variant calling algorithm, they just add context information to the resulting VCF.