Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
HaplotypeCaller (gvcf mode) on whole genome vs chromosome by chromosome
I'm currently running my first real use of GATK. I was worried about running HaplotypeCaller on whole geneomes given some of the reports I've seen on these forums about how long it can take to run. In contrast, I was pleasantly surprised with the current GATK it is proceeding well (~7 day estimate on dog wgs). But it seems it could be much faster if I divided it up by chromosome with the -L flag.
I see that the advice is to not use the -L flag for whole genome analysis . But the wording in that link seems open: it is not necessary, but if it would help efficiency it might be worthwhile.
I've found a related question on the forums here , but it seems the descrepancy discussed in that thread is suspected to be due to downsampling and not actually the result of a chromosome-by-chromosome use of HaplotypeCaller.
Again, I'm content with a ~7 day run time in order to take proper care of our data. I wouldn't want to sacrifice power or accuracy for a shorter runtime, but if there is really no trade-off, a chromosomal approach would be even better. So I'm curious if there is a downside to partitioning the HaplotypeCaller step by chromosome?