What is the difference between HaplotypeCaller and UnifiedGenotyper?
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2.7 years ago

Hi all,

I want to know what is the difference between HaplotypeCaller and UnifiedGenotyper for SNP Calling in the whole genome sequencing? In other words, which one is better for SNP Calling?

Best Regard

Mostafa

SNP • 2.6k views
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4
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2.7 years ago

Hello,

UnifiedGenotyper calls SNPs and indels on a per-locus basis. HaplotypeCaller discards the alignment information around a position where it suspects a variant and is doing local re-assembly with those reads. This has a high impact on calling indels and in repetitive regions.

UnifiedGenotyper isn't recommendet anymore. If you have to/like to choose between these both use HaplotypeCaller.

fin swimmer

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many thanks for your reply,

If we do not need indels, do you still recommend HaplotypeCaller?

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Yes. UnifiedGenotyper is only available for legacy reasons. The HaplotypeCaller has been tried and tested on a number of high impact projects such as ExAC. Additionally, here's a post from Geraldine on the GATK forum.

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Yes.

UnifiedGenotyper isn't available anymore in the current version of gatk.

fin swimmer

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Hello mostafarafiepour,

Don't forget to follow up on your threads.

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

Upvote|Bookmark|Accept

Please do the same for your previous posts as well.

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