broadinstitute/tag-public

Official workflows published by the Broad Institute's Genomics Platform Translation Analysis Group (TAG)

tag-public's Issues

Duplicate samples in Terra Workspaces

Hello! I noticed duplicate samples in a couple CMI workspaces & was hoping to find a way to rectify that!

1. We think that workspace broadtagteam/tag_264_MBC_Wagle_ULP-WGS has been merged already with broadtagteam/tag_94_MBC_Wagle_ULP-WGS. Can you verify this? If so, can we delete the old workspace (broadtagteam/tag_264_MBC_Wagle_ULP-WGS)?

2. There are 2 sample aliases in the workspace broadtagteam/tag_264_MBC_Wagle_ULP-WGS that are not in the other & are labeled "RP-1156_MBC_1_A_P_v1_WGS_OnPrem" and "MBCProject_1535_BLOOD" -- Can you verify that these 2 samples are the same? If not, what happened with RP-1156_MBC_1_A_P_v1_WGS_OnPrem?

3. Would it be possible to double check that the samples in the attached excel sheet are all duplicates to the Cote iChor workspace tag_190_Painter_Angio_MGH_ULP-WGS? If they all already exist there, can we remove them from the ASC space tag_42_113_CMI_Painter_Angiosarcoma?
   Terra_duplicates_tag_42_113_CMI_Painter_Angiosarcoma.xlsx

Thank you!

Error importing iChorCNA WDL script into DNAnexus

When I try to import iChorCNA_hg38.wdl into DNAnexus, I get the following error:

"WDL code is syntactically valid BUT it fails type-checking"

How can I fix this issue? Thank you!

GATK4 CNV + Mutect2 analysis request

Good morning TAG team,

I'd like to request the standard GATK4 CNV + Mutect2 analysis (P-ANA-0039) on a tumor/normal pair that was sequenced on the targeted cancer panel at 250xMTC in PDO-29201 (https://labopsjira.broadinstitute.org/browse/PDO-29201).

I am also requesting the same pipeline in tumor-only mode on the tumor-only sample (P-ANA-0038). Per Carrie Cibulskis's recommendation, we would like to include the exome PoN as the panel of normals and understand the caveats associated with doing this.

I have attached a list of SM-IDs for your reference and Carrie indicated that GP will cover the cost of analysis for the samples.

Please let me know if there are any questions or concerns with this request and thank you in advance for your assistance!
TAG analysis samples .xlsx