Generate vcf.gz file and its index file vcf.gz.tbi
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21
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8.3 years ago
lyz10302012 ▴ 360

Can anyone tell me how to generate vcf.gz file and its index file vcf.gz.tbi in 1000 Genomes Project?

ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/

vcf tabix • 98k views
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65
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8.3 years ago
bgzip -c file.vcf > file.vcf.gz
tabix -p vcf file.vcf.gz

tabix documentation

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Does the VCF have to be sorted like SAM/BAM does?

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Yes, tabix requires sorted input files. I don't think the sorting order matters, but records must be grouped together by rows.

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You mean numeric or alphanumeric by chromosome in ascending or descending order plus numeric by position ascending or descending order? I can't think how else sorting order could not matter.

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Yes. To clarify, I think you just need your chromosomes grouped together, and then records for each chromosome need to be sorted in ascending coordinate order.

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21
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8.3 years ago
Erik Garrison ★ 2.3k

I have a script which does this using a VCF stream on stdin:

#!/bin/bash

file=$1

bgzip >$file
tabix -f -p vcf $file

I found I was always writing the same lines over and over when indexing VCF files. You can use it like this:

cat uncompressed.vcf | bgziptabix compressed.vcf.gz
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9
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3.1 years ago
miaowzai ▴ 260
bgzip file.vcf       # or:   bcftools view file.vcf -Oz -o file.vcf.gz
tabix file.vcf.gz    # or:   bcftools index file.vcf.gz

this is convenient where tabix and bgzip are not installed. saw this from: https://github.com/samtools/bcftools/issues/668

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4
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3.6 years ago
ATCG ▴ 300
bgzip genotypes.vcf && tabix -p vcf genotypes.vcf.gz

see details if you need to:

https://qtltools.github.io/qtltools/pages/input_files.html

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