problem with bcftools isec

I have 2 vcf files and i am trying to run bcftools isec through galaxy but its throwing me the following error:
Expected the -p option

I don’t know how can I solve it?

Hi @Anas_Jamshed

What this tool expects technically:

  1. The headers are the same between all vcf inputs (same reference genome version/build).
  2. Each vcf has data lines.
  3. Those data lines contain the information that is being referenced in the query(ies) set on the tool form.

For this error, the message indicates that the tool was expecting to compute pairwise manipulations, but that flag didn’t get triggered. Did you input two different vcf files to the tool?

More help and examples about how to use this tool are at the bottom of the tool form, including link-outs to general usage sites supported by the authors. Most of what can be done line command is also available on this tool form for this tool.

We’ll need more information to help you more. See → Troubleshooting errors

yes I used 2 vcf files but how can I add -p trigger?

Hi @Anas_Jamshed

The tool should pick that up when there are two inputs as far as I know.


  1. What Galaxy server are you working at? URL
  2. Can you create and post a shared history link for more context?
  3. Screenshots might also work, but would need to contain the full page of the Job Parameters (with expanded datasets) and the command line, stdout, and stderr logs please.
  4. #1 #2 #3 are what the FAQ explains about eg how to ask questions with enough context so others can help.
  5. If you are using a tutorial, please also link that back in your reply, and note which step you are at.