GATK update

[shelby26]

Hi Misha,

For hard-calling SNPs using GATK, the function for GenomeAnalysisTK.jar / UnifiedGenotyper is no longer supported in the current version; instead it's replaced by HaplotypeCaller.

https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller

There are some file formatting and other issues with adapting UnifiedGenotyper to HaplotypeCaller in the updated version. Overall though was wondering if you had any suggestions on setting new parameters for HaplotypeCaller, vs. downloading and using the old version of GATK with UnifiedGenotyper, or running through ANGSD caller instead.

Thanks,
Shelby

[z0on]

Hi Shelby - thanks for alerting me! TBH I would simply use older gatk version (v3), they all seem to be available: GATK archive(< v3.8) : https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk/ Picard stand-alone: https://broadinstitute.github.io/picard/ I should probably make one of those dockers to package all the software tested for the 2bRAD pipeline… when I learn that. more procrasticoding for me :) Angsd is actually my preferred way these days, it is much neater (and way faster) than gatk, once you have bam files. My Angsd pipeline has nice quality exploration step that I did not have in the old gatk pipeline. My absolute favorite angsd-enabled application is PCAngsd, it nearly instantaneously makes a PCA, a structure plot, and even computes per-snp associations with structure. Misha

On Mon, Jul 26, 2021 at 1:11 PM shelby26 ***@***.***> wrote: Hi Misha, For hard-calling SNPs using GATK, the function for GenomeAnalysisTK.jar / UnifiedGenotyper is no longer supported in the current version; instead it's replaced by HaplotypeCaller. https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller There are some file formatting and other issues with adapting UnifiedGenotyper to HaplotypeCaller in the updated version. Overall though was wondering if you had any suggestions on setting new parameters for HaplotypeCaller, vs. downloading and using the old version of GATK with UnifiedGenotyper, or running through ANGSD caller instead. Thanks, Shelby — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZUHGHSTLHGLVBAR6ASQWTTZUYGXANCNFSM5A7Y6ZGQ> .

-- cheers Misha matzlab.weebly.com