How to extract variants falling in a genomic window from a VCF?

Question

[francois]

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:

ftp:/­/­ftp.­1000genomes.­ebi.­ac.­uk/­vol1/­ftp/­data_collections/­1000_genomes_project/­release/­20190312_biallelic_SNV_and_INDEL/­ALL.­chr20.­shapeit2_integrated_snvindels_v2a_27022019.­GRCh38.­phased.­vcf.­gz

The lead I was following was:

Unzipping the file.

Bgzip it with

bgzip chr20.vcf

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

(tab-separated)

---

I have also tried

vcftools --vcf chr20.vcf --bed oprwindow.bed --out trim --recode --keep-INFO-all

I get

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?

[Pierre Lindenbaum]

I have also tried

vcftools

vcftools is deprecated, use bcftools

[Pierre Lindenbaum]

tabix chr20.vcf.gz 1,000-20,000,000

the format for tabix is tabix file "chrom:start-end " and NOT tabix file "start-end "

furthermore may be it is is "chr20" not "20"

[francois]

Ah you know what, I had tried chr20:1,000-20,000,000 but not 20:1,000-20,000,000, which worked! Thank you.

So for anyone reading, correct commands are:

tabix -p vcf chr20.vcf.gz

tabix chr20.vcf.gz 20:1,000-20,000,000

Can write to a file as:

tabix chr20.vcf.gz 20:1,000-20,000,000 > trim.vcf

[Pierre Lindenbaum]

Unzipping the file. Bgzip it with

it's useless, the file are already b-gzipped.

$ wget -q -O - "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr20.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz" | file -
/dev/stdin: gzip compressed data, extra field