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tabix on 1000genome files

hi all,

i am trying to extract some data using tabix on the 1000genome files.

i downloaded the files using wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr16.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr16.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi

but then the tabix command below did not give me any results. any idea what did i do wrong?

tabix ALL.chr16.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz -h ch16:16000000-18000000

tabix vcf 1000genome
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by switch.reem • switch.reem

2 answers

the chromosome notation doesn't use the 'chr' prefix. try with 16:16000000-18000000

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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you so much. It worked. Totally didn’t see it coming

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written by switch.reem • switch.reem

1000G chromosomes are encoded without "chr" as prefix.

Try with 16:16000000-18000000

Also you can directly use tabix on the ftp stored files as :

tabix ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr16.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz 16:16000000-18000000
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written by Nicolas Rosewick Nicolas Rosewick

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