Can gaptools be run on only the subject phenotype files? about gaptools HOT 4 OPEN

Hi Daniel, Thank you for your feedback. You can run the tool with just the phenotype and id data files. Regards, Mike Michael Feolo Staff Scientist, dbGaP Team Lead National Center for Biotechnology Information Building 45, 4AN.12B, MSC 6514 Bethesda, MD 20894 Phone: 301.402.2874 Email: ***@***.*** From: Daniel E. Weeks ***@***.***> Sent: Wednesday, February 8, 2023 9:49 AM To: ncbi/gaptools ***@***.***> Cc: Subscribed ***@***.***> Subject: [EXTERNAL] [ncbi/gaptools] Can gaptools be run on only the subject phenotype files? (Issue #16) The gaptools documentation mentions only two required files: the subject consent and the subject sample map files. So I was wondering if it could be run on input that contains those two plus the subject phenotype files without providing any genotype data? Or is it required that genotype data be present for a run of gaptools? For example, if I run it on a made-up test data set with this json below, it doesn't do anything beyond generating a metrics-CHECK_METADATA_FILES.json file containing the following: [ { "dag_id": "GapTools", "run_id": "2023-02-08-13-57-32", "dag_task": "CHECK_METADATA_FILES", "metric_name": "dag_run_start_time", "metric_value": "2023-02-08 13:57:45", "metric_object": "" } ] Input meta data json file { "NAME": "Example 1", "FILES": [ { "name": "ExampleConsent_DS.txt", "type": "subject_consent_file" }, { "name": "ExampleConsent_DD.xlsx", "type": "subject_consent_data_dictionary_file" }, { "name": "ExampleSSM_DS.txt", "type": "subject_sample_mapping_file" }, { "name": "ExampleSSM_DD.xlsx", "type": "subject_sample_mapping_data_dictionary_file" }, { "name": "DS_Example.txt", "type": "phenotype_ds" }, { "name": "3b_SSM_DD_Example1.xlsx", "type": "phenotype_dd" } ] } - Reply to this email directly, view it on GitHub<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fncbi%2Fgaptools%2Fissues%2F16&data=05%7C01%7Cfeolo%40ncbi.nlm.nih.gov%7C43f914e3761a4e19bbb508db09e3a785%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638114645599157878%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QG86RXA94L9fovDmEiKsWXb6akK1tlZKrMU4L5uyp7U%3D&reserved=0>, or unsubscribe<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FARSL2T4XIFSNO57CWQFRPPDWWOW6XANCNFSM6AAAAAAUVLKAK4&data=05%7C01%7Cfeolo%40ncbi.nlm.nih.gov%7C43f914e3761a4e19bbb508db09e3a785%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638114645599157878%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ur6M5044Q3uLza9OLT%2BpcNerRhjfaq3VjcqxL%2FZTYWk%3D&reserved=0>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Hi Daniel, Thanks for following up. You beat us to it. We will take your feedback into account to make the documentation better. Regards, Mike From: Daniel E. Weeks ***@***.***> Sent: Thursday, February 9, 2023 5:56 PM To: ncbi/gaptools ***@***.***> Cc: Feolo, Mike (NIH/NLM/NCBI) [E] ***@***.***>; Comment ***@***.***> Subject: [EXTERNAL] Re: [ncbi/gaptools] Can gaptools be run on only the subject phenotype files? (Issue #16) I found my mistake: I didn't notice this line in the instructions: "The file has to be named metadata.json" so it was failing because I had named it 'Example1.json' instead. Suggestion: I made this mistake in part because I assumed this option in the example command: