Entering edit mode
8.2 years ago
jan.breitling
▴
10
Hi
The vcf file I am using is here: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/vcf_with_sample_level_annotation/
It is a annotated vcf fort the 1000G. I am looking to extract the following information
-Position of LOF mutations -Position of Coding mutations -Position of functional noncoding -Position of unannotated vars
I really don't know how to do that - is there any simple way to to do that? I would be really grateful! Like in awk, python, R or so?
Try Annovar or KGGSeq
well - sorry but how does that help?
Those two programme can annotate all the SNPs within the VCF. Based on the annotation, you can then filtered out all the LOF mutations, Coding mutations etc.