This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Create A Tbi File From Vcf

hi all. i am generating a vcf file as the end result of my processing and i want to perform an interval query. since, tabix can do that, what is the way to generate a tabix (.tbi) file for the vcf file that is generated?

the commands would help a lot.

thanks in advance.

ashwin

vcf
• 21,065 views • link
updated by Biostar Biostar • written by win win

1 answer

I'll just answer the same thing as Pierre for the sake of closing the question.

A tbi file is a tabix index file. To generate it invoke the tabix program with the -p flag like so:

tabix -p vcf myfile.vcf
• 0 views • link
written by Istvan Albert Istvan Albert

Log in to answer this question.

More posts like this
  • display vcf after giraffe alignment on IGV
    written by Michal • Michal
    I performed Giraffe alignment to map reads to the HPRC pangenome, resulting in a gam file. Subsequently, I utilized the following commands to generate a …
  • GATK joint genotyping
    written by win win
    Hi all, i am struggling a bit with preparing a cohort genome vcf file for joint genotyping using GATK. I tried with 30 BAMs from …
  • tabix indexing issue
    written by bjlemmer • bjlemmer
    I am unable to view my data which I was able to view and manipulate with similar commands prior to this. Running on a Linux …
  • Lift-over on a VCF
    written by win win
    <p>Hi all,</p> <p>I have a VCF file that was generated using HG18 and I want to convert it to VCF but that has HG19 data.</p> …
  • Bed File Coordinates
    written by win win
    <p>Hi all, In a spreadsheet i have my list of rs# with their chromosomal number and locations. I want to generate a BED file for …
  • Homozygous Ref Calls And No Calls
    written by win win
    <p>Hi all, I was wondering if someone could help. </p> <p>I am generating a vcf file based on the following command chain.</p> <p>samtools sort eg2.bam …
  • Use tabix with a list of regions
    written by win win
    Hi all, I need to use *tabix* for a project and the following is the syntax that is used, for e.g. tabix -fhftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr12.phase1.projectConsensus.genotypes.vcf.gz 12:2345295-2345295 > …
  • Variant Sites Not Listed In Vcf
    written by win win
    <p>hi all hope someone can help. The .vcf file generated after SNP calling contains variants with genotypes of 0/1 or 1/0 or 1/1.</p> <p>does this …
  • Variant Sites In The Human Genome
    written by win win
    <p>hi all, i wanted to query for all sites in the human genome where variants occur. for e.g if we use dbSNP in vcf format …
  • Help Using Tabix
    written by Pi • Pi
    <p>Greetings</p> <p>How do you view the tbi file generated by tabix? I am using tabix v0.2.5 to index a local BED file of gene positions. …