GATK 4.0 HaplotypeCaller vs. GATK 3.x UnifiedGenotyper

[ksil91]

@z0on
Since UnifiedGenotyper was replaced in GATK 4+ with HaplotypeCaller, any thoughts about changing the 2bRAD genotyping protocol for high-coverage data? It seems like HaplotypeCaller mostly improves with calling indels, and may change some filtering options.

[z0on]

Hi Katherine - with 36-b reads that never overlap partially but just stack in fully overlapping piles, I doubt there would be any advantage of HaplotypeCaller (I am assuming it infers haplotypes from overlapping reads, please correct me if I’m wrong). I am actually not sure what effect our weird read placement woudl have on HaplotypeCaller. This is why I did not go that route with the original GATK pipeline. If you are willing to give it a shot, please let me know how it went! cheers Misha

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On Apr 23, 2019, at 3:19 PM, Katherine Silliman ***@***.***> wrote: @z0on <https://github.com/z0on> Since UnifiedGenotyper was replaced in GATK 4+ with HaplotypeCaller, any thoughts about changing the 2bRAD genotyping protocol for high-coverage data? It seems like HaplotypeCaller mostly improves with calling indels, and may change some filtering options. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZUHGH3OMNWAW3TDBMNZGDPR5VLVANCNFSM4HH6CI5Q>.

[ksil91]

Thanks! I might try it with both to see if there are differences. Cheers!