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