Jose M Soto
- Total activity 14
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 0
- Subscriptions 4
Activity overview
Latest activity by Jose M Soto-
Jose M Soto created an article,
Array Imputation v2 Pipeline Overview
Jump to:Inputs and OutputsInput ValidationQuality ControlPhasingImputingTroubleshooting A detailed description of the pipeline can be found at the WARP website.Inputs and OutputsInputsThe All of Us...
-
Jose M Soto created an article,
Pipeline Versions
Low-Pass WGS ImputationV1This pipeline is described in Low-Pass WGS Imputation v1 Pipeline Overview. When new versions are added, changes will be described here.
-
Jose M Soto created an article,
Input Requirements
Before submitting a job, ensure that your input cram manifest meets these conditions: has 3 columns with these headers: sample_id, cram_path, cram_index_path counts of CRAMs, CRAIs, and sample IDs...
-
Jose M Soto created an article,
Low-Pass WGS Imputation v1 Pipeline Overview
Jump to:Inputs and OutputsInput ValidationQuality ControlPhasingImputingTroubleshooting A detailed description of the pipeline can be found at the WARP website.Inputs and OutputsInputsThe All of Us...
-
Jose M Soto created an article,
Pipeline Versions
Array ImputationV2There are two major differences between v1 and v2. One is v2 is using a left aligned reference panel and the other is the imputed hom ref variants have been moved to their own si...
-
Jose M Soto commented,
Hey Jaewon,DR2 and R2 are not exactly the same in all contexts but yes you can treat them as identical values for QC filtering purposes. Poorly imputed variants will be closer to 0 for both.Hope t...
-
Jose M Soto commented,
It seems unlikely we would publish the summary metrics you mentioned unless there was a larger interest from users. If this was something you really wanted, researcher workbench could be used to g...
-
Jose M Soto commented,
Thank you for explaining your use case! FISS uses gcloud to auth so if your environment is able to utilize FISS you should also be able to auth to our cli using terralab login-with-oauth $(gcloud ...
-
Jose M Soto commented,
Hey Christina,There is currently no way to automate authenticating to the client without some kind of manual intervention every ~2 weeks as this is when tokens generated by the cli expire. Within ...
-
Jose M Soto created an article,
Array Imputation v1 Pipeline Overview
Jump to:Inputs and OutputsInput ValidationQuality ControlPhasingImputingTroubleshooting A detailed description of the pipeline can be found at the WARP website.Inputs and OutputsInputsThe All of Us...