tabix on 1000genome files

Question

[switch.reem]

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

Answer 1

[Pierre Lindenbaum]

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

[switch.reem]

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

Answer 2

[Nicolas Rosewick]

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