This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
Scatter Gather on HaplotyperCaller - Scatter on locus or intervals ?
I am now learning to use WDL esp for running Scatter Gather on HaplotyperCaller
1) In this example, https://software.broadinstitute.org/wdl/userguide/article?id=7614 , scatter gather is done on default setting of Haplotyer Caller (i.e. by locus)
2) On the other hand, in this example, https://github.com/broadinstitute/wdl/blob/develop/scripts/broad_pipelines/PublicPairedSingleSampleWf_160720.wdl, scatter gather was done on a specific interval.
Question 1) Is there an advantage of running scatter-gather over an interval instead of "by locus" ?
Question 2) Suppose I wanted to run scatter gather on HaplotypeCaller (to generate raw VCF file) and I want it to be scattered per chromosome, could you give me some advice on how I can do that ?