Kishwar Shafin

@rickymagner, yes, I can confirm that DeepVariant only considers ACGTN as valid bases.

Hi @chilampoon , I was unable to resolve this issue, I am marking this as won't fix.

@aguygarner , sorry for forgetting to reply to this issue. The solution is to do `--dry_run` and run each command independently. Please reopen if this is still an issue for...

@ColinR01 , Is it possible to provide the input files to reproduce this result?

Hi @ColinR01 , Please try the following docker that has the patch incorporated that should fix your issue: ```bash docker pull google/deepvariant:CL602468145 docker pull google/deepvariant:CL602468145-gpu ```

@ColinR01 , Can you please try the v1.6.1 docker? If the issue isn't resolved, please feel free to reopen this bug.

Oh, sorry, I misread the message. Is there a way you can see the depth of your sequencing in the region of interest on IGV or by running `samtools depth`?...

@kiflu-23 , in that case you'll have to run each step independently. First, collect all the commands that are run by running the `run_pepper_magin_deepvariant` with `--dry-run` command. Then for each...

hi @yuukiiwa , Unfortunately, making PEPPER conda ready is a big lift and we don't have the resources or manpower to do it currently. We will continue to support this...

Hello @shinlin77 , Can you provide a little more information about this? 1) How (not why, sorry) are you running GATK after clair3? Would it be the case that you...