In GATK, SNPs and INDELs are called separately or together?

Question

[Chen Sun]

In GATK, SNPs and INDELs are called separately (i.e. they are using different statistical models and different features) or they are called together(in one round with the same statistical model and features).

Thanks.

Answer 1

[WouterDeCoster]

GATK has a Unifiedgenotypecaller which does calling separately, and the HaploTypecaller which does both together.

[Medhat]

and using HaploTypecaller is highly advised by GATK documentation

[WouterDeCoster]

Yes absolutely! Should have made that clear in my answer.

Answer 2

[Petr Ponomarenko]

It depends on what you are using GATK for and what you are using in GATK package for variant calling. For example, HaplotypeCaller is trying to find haplotypes likelihoods and uses these to find genotype likelihoods. https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php