variant Recalibrator, -an option

Question

[noeD]

Hello!

I would like to understand the -an option in Variant Recalibrator of GATK. (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php)

For example, If I use the -an DP option, what will GATK do?

Thank you in advance

Answer 1

[Pierre Lindenbaum]

the an is a set of annotations that will be used from the VCF to "learn' what is a good/bad variant.

for example if a majority of the "bad" variants have DP<20 and the "good" have DP>=20, this model will be used to take a decision.