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Question: VCFfilter returns 0 output when the two filtering criteria applied
2
gravatar for u9urtoprak
4 months ago by
u9urtoprak • 20
u9urtoprak • 20 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 • 153 views
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modified 4 months ago by Jennifer Hillman Jackson ♦ 25k • written 4 months ago by u9urtoprak • 20
0
gravatar for Jennifer Hillman Jackson
4 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 4 months ago by u9urtoprak • 20
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