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Question: SNPsift filtering problem
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gravatar for sara.mehrabi
17 months ago by
sara.mehrabi • 40
Sweden
sara.mehrabi • 40 wrote:

Dear All.

I would like to filter my VCF file with SNPsift for DP, Quality, SRP, SAP and Effect (remove all the intergenic_region(MODIFIER||||||||||1).

The first problem is that I can not filter for all of them together, I followed the instruction, but its not working. I can just filter for one of them at the time.

the second problem is I can not filter for Effect, I tried several things, but its not working.

I appreciate your thought or experience.

Best, Sara
snpsift filtering • 558 views
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written 17 months ago by sara.mehrabi • 40
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gravatar for Guy Reeves
17 months ago by
Guy Reeves • 1.0k
Germany
Guy Reeves • 1.0k wrote:

First step, are all the variables yo are filtering with present in your vcf. Have you annotated your .vcf e.g.. with SNPeff? When working with SNPsift it is best to put in simple expressions first, check the output to make sure it makes sense and only then to attempt to combine expressions. This is especially useful for less experienced users, the syntax of very complex expressions is often not trivial. Go stepwise. Cheers Guy

ADD COMMENT • link written 17 months ago by Guy Reeves • 1.0k
1

First step: yes they are available. yes I did annotate with SnpEff. I am able to filter for DP, Quality, SRP, SAP one by one, but not all together. exp: I filter for DP, then filter for QUAL on the DP filtered file and so on and it worked. but still I am not able to filter for Effect. Thanks.

ADD REPLY • link written 17 months ago by sara.mehrabi • 40

First part are you placing each filter within (). unless specified this makes each filter an AND. So for (DP>23) (QUAL>200) only sites which pass both filters will be retained. If you want to use OR then you need to look at "|". look at the the instructions on http://snpeff.sourceforge.net/SnpSift.html

they are vey good.

About filtering the 'ANN' ' field where I guess your 'intergenic_region' annotation is have you read the section in the above link?

ADD REPLY • link written 17 months ago by Guy Reeves • 1.0k
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