Difference in Haplotypecaller in GATKv4 Vs Gatk3.7

Question

[NB]

Hello

Does anyone know the difference/updates for Haplotypecaller in GATK v4 vs GATK 3.7 ?

I am not able to find anything specific in terms of its algorithm or major changes in the walker on the GATK website

Thanks,

[Kevin Blighe]

You should post on the GATK support forum. There, it should get a swift response from Geraldine.

[NB]

Yes, done that already

[Kevin Blighe]

Great thank you, Nandini, for linking these up.

Answer 1

[lffu_0032]

the algorithm of HC between gatk-3.7 and gatk-4.0 is almost same, you can see from: https://gatkforums.broadinstitute.org/gatk/discussion/10925/9-things-youve-been-dying-to-know-about-the-haplotypecaller-paper.

Q: How does the methodology compare to GATK4?

A: The GATK engine that parses the BAM and “shards” the data to pass to the tools has been rewritten for improved efficiency over GATK3, and the HaplotypeCaller code has been refactored for better organization and readability. So there's a lot that is different in terms of software implementation. However the algorithms and equations presented in the manuscript remain the same, so overall the paper's description of how the HaplotypeCaller operates also applies to the GATK4 beta version, and it is appropriate to use it as a citation for results derived from versions up to the current beta (4.beta.6).

[NB]

thank you @lffu_0032 , the link provided is useful!