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Question: Galaxy VCF Combine combines only to chr13
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gravatar for stanedav
2.9 years ago by
stanedav • 0
stanedav • 0 wrote:

Hello, 

I am using Galaxy with vcflib (Garrison, Erik (2015). vcflib). I have two vcf files, which I want to combine together. Problem is, that I will get merged file from two files, but only to chr13 (I have human data with 23 chromosomes. Could somebody help me, how to solve this issue?

Example files are here:

https://www.dropbox.com/s/k9cplypbmiqai6z/file1.vcf?dl=0

https://www.dropbox.com/s/9uxn9xw8cvodanh/file2.vcf?dl=0

I tried public Galaxy server and also our local Galaxy server, but with same output.

Thanks for help
combine vcf galaxy • 760 views
ADD COMMENT • link •
modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by stanedav • 0
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gravatar for Jennifer Hillman Jackson
2.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Please share a link to the history with the unexpected result, as executed on http://usegalaxy.org, with galaxy-bugs@list.galaxyproject.org. Make certain that all datasets are undeleted and please also include a link to this biostar post. Specifying which dataset result you find problematic will also help (if there is other work in the history).

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k
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