extract vcf subinfo
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?
• 2,389 views
•
link
updated
by
Ram
•
written
by
jan.breitling •
•
written
by
jan.breitling •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Error getting the genome on clinvaR
written by camillab. •
-
Downloading 1000genome phase 3 data in 38 build
written by AVA •
-
Comparison of allele frequencies between population
written by elisheva
-
1000 Genome Project Structural Variants for Illumina
written by Yasin Uzun •
-
tabix on 1000genome files
written by switch.reem •
-
1000 genomes missing SNPs on chr X in GRCh38
written by b_ha •
-
Where can I find the reference files for the 1000 Genome project VCF data?
written by caggtaagtat
-
snps/indels with individual genotypes from 1000 genomes ftp site
written by lait
-
How to get IDs of family trios in 1000 genomes project?
written by GabrielMontenegro
-
How to download SNP list of 1000 Genome
written by sinorenjianyi •
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.