Question: Difference in Haplotypecaller in GATKv4 Vs Gatk3.7
0
gravatar for Nandini
4 months ago by
Nandini780
London
Nandini780 wrote:

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,

gatk haplotypecaller • 264 views
ADD COMMENTlink modified 4 months ago by lffu_003230 • written 4 months ago by Nandini780

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

ADD REPLYlink written 4 months ago by Kevin Blighe39k

Yes, done that already

ADD REPLYlink written 4 months ago by Nandini780

Great thank you, Nandini, for linking these up.

ADD REPLYlink written 4 months ago by Kevin Blighe39k
2
gravatar for lffu_0032
4 months ago by
lffu_003230
lffu_003230 wrote:

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).

ADD COMMENTlink modified 4 months ago • written 4 months ago by lffu_003230

thank you @lffu_0032 , the link provided is useful!

ADD REPLYlink written 4 months ago by Nandini780
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