VCF combine only showing chromosome 1 in the output

Question: VCF combine only showing chromosome 1 in the output

17 months ago by

Hi, I tried many times to combine 32 .vcf files in Galaxy using VCF Combine. In the output file I can see only a few lines (chromosome 1). I downladed the file and the downloaded file also contain only few lines in it. Using the edit attributes tool I edited the Number of comment lines to larger numbers, and also did unclick, so that it does not have any limit. But, everytime it showed up the same result. If you could help me with this it will be highly appreciated.

Thank you, Sri

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modified 16 months ago by Guy Reeves • 1.0k • written 17 months ago by drsrideviunni • 20

Please help me if any one has a solution for this. Hope this problem is common for everyone who uses galaxy for this application.

ADD REPLY • link written 17 months ago by drsrideviunni • 20

16 months ago by

drsrideviunni • 20

drsrideviunni • 20 wrote:

Hi, Thank you for the reply to my post. I sorted the .vcf files using vcf sort of Galaxy and ran the vcf combine. But the results are still the same. In my .vcf and sorted files I can see all the other chromosomes, but it is not showing up in the combined file. I really appreciate your help. Sri

ADD COMMENT • link written 16 months ago by drsrideviunni • 20

Where are you working? http://usegalaxy.org? If so a bug report can be sent in and we can review. This is the only report of a problem with the tool so far that didn't involve a memory problem (tool ran out of resources). https://galaxyproject.org/issues/#usage-problem-reporting

I am wondering if the tool is running out of memory in your case however some error or warning message should result from that situation now.

ADD REPLY • link modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson ♦ 25k

Yes, I am working on http://usegalaxy.org When I do the VCFcombine I do not get any error messages. So there is no bug report available. The program runs perfectly, and I get a single file as output which contains all my samples, but it shows only the top 130 lines (chromosome 1, not sure if it is complete data of chromosome 1). Thanks

ADD REPLY • link written 16 months ago by drsrideviunni • 20

16 months ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

Hi Siri Can I sugest you try another tool. I am assuming that you are using usegalaxy.org. So I suggest you try "Combine Variants (Galaxy Version 0.0.4)" and see if you get the same result.

If you are using your own galaxy instance there are a number of other tools you could try Tell us what happens. Cheers Guy

ADD COMMENT • link modified 16 months ago • written 16 months ago by Guy Reeves • 1.0k

Agree - this can be an alternative depending on the desired output (merged vs combined).

ADD REPLY • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

what is the difference between combine versus merge VCF?

ADD REPLY • link written 16 months ago by Guy Reeves • 1.0k

Hello, As suggested I did the Combine variants. I tried both .vcf files and also the sorted files. This created error messages.
Unlike VCFCombine (which produces a single file), Combine Variants program create separate files for each input file, which I do not understand why. Please suggest me if anything can be rectified from my end. Thank you Sri

ADD REPLY • link written 16 months ago by drsrideviunni • 20

The errors might be informative. Would you send one in as a bug report please? This will help get to the bottom of the problem (core tool issue vs input data problem vs usage clarification vs tool running out of memory). A shared history link can also be sent in from any history at http://usegalaxy.org, even if there are not red error datasets, directly to galaxy-bugs@lists.galaxyproject.org.

The simplest way to do this is: if the runs from the two tools are in different histories, use the one with the red error to send in a bug report and just include a shared history link to the other history in the comments. Note the datasets involved and make sure they are left in an undeleted state (inputs and outputs). Please also include a link to this Biostars post so we can associate the two. I didn't see any that look like yours so far, so correct me if one was sent already with this information - maybe by replying to the galaxy-bugs email address with the extra info, even if only a link to this post (if all runs are in that same history).

How to send in a bug report: https://galaxyproject.org/issues/#usage-problem-reporting
How to generate a shared history link: https://galaxyproject.org/learn/share/

ADD REPLY • link modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson ♦ 25k

Hello, I have already sent the red error bug report yesterday. Also, I tried to share the history through galaxy-bugs@lists.galaxyproject.org. However, it shows invalid galaxy user ID. Pls suggest me if there is another email ID.

Thank you.

ADD REPLY • link written 16 months ago by drsrideviunni • 20

I just tried this tool and I get only one output file and one log file.

ADD REPLY • link written 16 months ago by Guy Reeves • 1.0k

Could you please guide me the steps so that I can also follow the same method.

Thank you.

ADD REPLY • link written 16 months ago by drsrideviunni • 20

Combining two VCFs I did this

https://www.dropbox.com/s/cm0z305ezc3yxyo/Screen%20Shot%202017-07-13%20at%2007.58.01.png?dl=0

and got

https://www.dropbox.com/s/idr09tsb5ieezx1/Screen%20Shot%202017-07-13%20at%2007.58.24.png?dl=0

!There us a difference between combine and merge !

ADD REPLY • link modified 16 months ago • written 16 months ago by Guy Reeves • 1.0k

16 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Try using the tool VCFsort first then combine. It may be that your data is not ordered.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

ADD REPLY • link written 16 months ago by drsrideviunni • 20

Hello, I am having the same problem as the original poster (VCF combine output only showing data up to chromosome 3), and trying this solution did not work. Were there any updates or conclusion to this issue? Best, Kelsey

ADD REPLY • link written 7 weeks ago by kelseyca • 0

16 months ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

If you post the shared link to the history here that may also help me help you.

ADD COMMENT • link written 16 months ago by Guy Reeves • 1.0k

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