AD for 0/0 site

ying_sheng_1

Hi Geraldine,

When I used UnifiedGenotyper to emit all sites, for 0/0 site, I only got GT and DP tags. Is it possible to get AD tag for these sites and get actual depth for these sites, not downsampling coverage (I can see the maximum value is 200 if I ask for downsampling to 200 when running UnifiedGenotyper)

thanks!

Sheila

@ying_sheng_1‌

Hi,

AD cannot be annotated for 0/0 sites. In any case, it would be downsampled. The best thing to do is use DepthOfCoverage or DiagnoseTargets. Please read about them here:

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

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

You can use the VCF as the intervals list to get total depth counts at those sites.

-Sheila

ying_sheng_1

Thanks!

Ying