mpileup2sync

Question

[Hayler Edu]

Hello there, I'm new to doing this type of analysis. I'm trying to convert a mpileup file into the synchronized file format (sync) but I have a problem using the script that I found.

This is the script:

mpileup2sync --input pools_all.mpileup --output pools_all.sync --fastq-type sanger --min-qual 20 --threads 15

When I execute the script the output shows me that:

mpileup2sync: command not found

I search for how to install mpileup2sync but I don't find any information, can someone help me by telling me how can I install mpileup2sync?

[Ram]

That's not a script, that's a command. Where did you find it?

Did you Google "mpileup2sync"? If you did, you would not have spelled popoolation2 the way you did. It looks like you did not do any decent level of searching before you created the post here, because the solution to your problem is pretty easy to find once you get to the popoolation2 tool page.

First 2 results on Google include your question and the answer to it:

Clicking on the first link takes me to the sourcecode page. I tried the svn checkout method and it did not work. Next, I went to the main page of the repo to see if they have any new announcements and there, I saw the download link, which I can use to download the source code.

Finding the solutions to our problems is as simple as that - taking baby steps into uncharted territory until those steps become easy when we gain confidence.