Question: VCFfilter returns 0 output when the two filtering criteria applied
2
gravatar for u9urtoprak
12 weeks ago by
u9urtoprak20
u9urtoprak20 wrote:

Hello,

I am taking the course on coursera. For the final project we have to Identify DNA polymorphic sites.

I have completed most of the steps but when I try to filter my vcf file to find ins and del it returns 0 lines. When I do it separately no problem.

I tried every possible solutions, read forums, documentations and so on.

What I did I add filters with button and did not work, and I tried with combining two filtering criteria in a same line with & operator also did not work.

Any suggestions about this point?

question vcffilter filters • 97 views
ADD COMMENTlink modified 12 weeks ago by Jennifer Hillman Jackson25k • written 12 weeks ago by u9urtoprak20
0
gravatar for Jennifer Hillman Jackson
12 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Please use the most current tool version if not already: VCFfilter (Galaxy Version 1.0.0_rc1+galaxy1)

The prior tool version included in the Coursera tutorials was removed from Galaxy Main https://usegalaxy.org server for technical reasons.

Current open issues with this tool (usage/tool form help related): https://github.com/search?q=org%3Agalaxyproject+vcffilter&type=Issues

I'll do some testing to determine if using multiple filters with the updated tool is either 1) a usage issue (and post back help) or 2) a new tool bug (a new issue ticket will be part of this).

Thanks for reporting the problem, more feedback on Monday. Jen, Galaxy team

ADD COMMENTlink written 12 weeks ago by Jennifer Hillman Jackson25k

Hi,

Thank you Jen, could you please try it with add filters TYPE = ins then add 2nd filter TYPE = del . This way did not work for me. So I did it separately to move on.

Looking forward to your feedback.

ADD REPLYlink written 12 weeks ago by u9urtoprak20
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