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Question: EFF (Effect) filtering
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gravatar for sara.mehrabi
17 months ago by
sara.mehrabi • 40
Sweden
sara.mehrabi • 40 wrote:

Hi All,

I would like to filter my VCF file for Effect, exp: delete all the intergenic_region. I tried all the possibility I could think of and what ever they wrote as help, but nothing ! :( I wonder if some one has some solutions or similar experience? Thanks in advance.

Best/Sara
effect snp filter • 421 views
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modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 17 months ago by sara.mehrabi • 40
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gravatar for Jennifer Hillman Jackson
16 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool Select can be used with a regular expression to perform filtering on most any value that you want. I see the help Guy gave you in the other post, so am not sure if this is still an open question or not, but wanted to let you know about alternative options to the tools in NGS: VCF Manipulation

When working with a VCF dataset, save the header off into another dataset (also filtered out with the same tool) then use the tool Concatenate to place it back on top of the filtered dataset if you are not using tools from the group VCF Manipulation.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k
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