I am trying to extract the variants falling within a given genomic window from a VCF file.
I have tried pretty much all suggestions from Post not found, but my terminal is staying mute!
The file in question is:
The lead I was following was:
Unzipping the file.
Bgzip it with
Index it with
tabix -p vcf chr20.vcf.gz
Then I have tried
tabix chr20.vcf.gz 1,000-20,000,000 tabix -R window.txt chr20.vcf.gz tabix -R window.bed chr20.vcf.gz
window.txt and window.bed are:
chr20 1000 20000000
I have also tried
vcftools --vcf chr20.vcf --bed oprwindow.bed --out trim --recode --keep-INFO-all
VCFtools - 0.1.16 (C) Adam Auton and Anthony Marcketta 2009
Parameters as interpreted: --vcf chr20.vcf --recode-INFO-all --out hey --recode --bed window.bed
Error: VCF version must be v4.0, v4.1 or v4.2: You are using version VCFv4.3
What am I doing wrong? Any lead?