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/
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lyz10302012
4 answers
bgzip -c file.vcf > file.vcf.gz
tabix -p vcf file.vcf.gz
Yes, tabix requires sorted input files. I don't think the sorting order matters, but records must be grouped together by rows.
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.
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
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
bgzip genotypes.vcf && tabix -p vcf genotypes.vcf.gz
see details if you need to:
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