Advanced use of snpEff

Question

[zion22]

Hello I have two questions for this wonderful forum: 1- I have results of snpEff (vcf files) but some of you know the command to generate the statistics from this file, normally snpEff does it when I run it, but I just want the statistics without running the whole program. 2- How can I filter the snpEff results by functionality or effects e.g.: only no synomims Thanks a lot

[Kevin Blighe]

Can you show the snpEff command that you used? Also, can you paste a few lines of your VCF?

[zion22]

Hi I used this command snpEff -c snpEff.config GRCh37.75 variants_.vcf.gz" > variants_.snpEff.vcf

I know that this way i get three output files, the annotated vcf file, a text file summarizing the number of variant types per geneand and HTML file containing summary statistics, but i just want to know how to get HTML file again from "variants_.snpEff.vcf" without the necessity to run everything again. Also I want to know how can I filter the snpEff results by functionality or effects e.g. only no synomims

[Kevin Blighe]

I am not sure that you can re-run the command to only generate the HTML file - are you not in a position to re-run the command?

For filtering the VCF, you can use the in-built functionality: http://snpeff.sourceforge.net/SnpSift.html#filter. Alternatively, you can simply use a combination of BCFtools and carefully-constructed grep commands in order to filter the VCF yourself.

Answer 1

[Arup Ghosh]

1)If you are looking for the HTML stats file I guess you will need to run the program completely just don't store the output if you don't need it.

2) There is another program that comes with snpEff called SnpSift, you can use it for filtering and statistical analysis.

SnpSift filtering documentation.

[Kevin Blighe]

Thanks for answering, arup