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

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.

gatk snp indel variant
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updated by Biostar Biostar • written by Chen Sun Chen Sun

2 answers

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

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written by WouterDeCoster WouterDeCoster

and using HaploTypecaller is highly advised by GATK documentation

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written by Medhat Medhat

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

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written by WouterDeCoster WouterDeCoster

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

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written by Petr Ponomarenko Petr Ponomarenko

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