can gatk4 add indel realignment function and complex variants
Answered
Can you please provide
a) GATK 4.1.8.0
in this post, you confirm the value of indel realignment, even haplotypecaller incleding some of that, so why gatk not including it, we want a good command, but not continous new command that not much useful, I still do not know why gatk3 can include indel realignment, but why gatk4 can not. ,command like calling complex variant is also we needed, I think developers may pay some time on this, thanks a lot
https://github.com/broadinstitute/gatk-docs/blob/master/blog-2012-to-2019/2016-06-21-Changing_workflows_around_calling_SNPs_and_indels.md?id=7847
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Official comment
Hi that girl,
I have posted a more comprehensive response at another similar post. Please see that comment for more details: https://gatk.broadinstitute.org/hc/en-us/community/posts/4410638253723-Indel-realignment-GATK4?page=1#community_comment_4411135563419
Best,
Genevieve
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