Question: Difference in Haplotypecaller in GATKv4 Vs Gatk3.7
0
gravatar for Nandini
13 months ago by
Nandini830
London
Nandini830 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 • 544 views
ADD COMMENTlink modified 13 months ago by lffu_003240 • written 13 months ago by Nandini830

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

ADD REPLYlink written 13 months ago by Kevin Blighe52k

Yes, done that already

ADD REPLYlink written 13 months ago by Nandini830

Great thank you, Nandini, for linking these up.

ADD REPLYlink written 13 months ago by Kevin Blighe52k
2
gravatar for lffu_0032
13 months ago by
lffu_003240
lffu_003240 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 13 months ago • written 13 months ago by lffu_003240

thank you @lffu_0032 , the link provided is useful!

ADD REPLYlink written 13 months ago by Nandini830
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