search

broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
https://broadinstitute.github.io/gatk-sv/
BSD 3-Clause "New" or "Revised" License
171 stars 71 forks source link

Need clearer instructions on each parameter for GATK-SV-single-sample #443

Open jasonbhn opened 2 years ago

jasonbhn commented 2 years ago

Hi, I'm trying to use the workspace help-gatk/GATK-Structural-Variants-Single-Sample](https://anvil.terra.bio/#workspaces/help-gatk/GATK-Structural-Variants-Single-Sample to call SVs on a few individuals I have. I decided to use the 1000G reference panel on https://console.cloud.google.com/storage/browser/gatk-sv-resources-public?authuser=0 but this still doesn't include some items that seems necessary:

  1. sd_locs_vcf
  2. sv_pipeline_updates_docker would appreciate a concise explanation of what those are thank you
mwalker174 commented 2 years ago

Hi @jasonbhn sorry for that. The sd_locs_vcf can be found here and you can just use the sv_pipeline_docker for sv_pipeline_updates_docker. We'll look into updating the workspace.

cwhelan commented 2 years ago

Hi @jasonbhn -- it looks like there's a an issue with the workspace data in the single sample pipeline featured workspace. To make sure you are using the right parameters (especially all the docker files) for everything I'd recommend updating your workspace data by uploading this tsv file into the data tab of your workspace. We'll work on getting the feature workspace updated with the correct values.