How do I get a genomic region sub-section of your files?

You can get a subsection of the VCF or BAM files using the Ensembl Data Slicer tool. This tool gives you a web interface requesting the URL of any VCF file and the genomic location you wish to get a sub-slice for. This tool also works for BAM files. This tool also allows you to filter the file for particular individuals or populations if you also provide a panel file.

You can also subset VCFs using tabix on the command line, e.g.

tabix -h 2:39967768-39967768

Specifications for the VCF format, and a C++ and Perl tool set for VCF files can be found at vcftools on sourceforge

Please note that all our VCF files using straight intergers and X/Y for their chromosome names in the Ensembl style rather than using chr1 in the UCSC style. If you request a subsection of a vcf file using a chromosome name in the style chrN as shown below it will not work.

tabix -h chr2:39967768-39967768

You can subset alignment files with samtools on the command line, e.g.

samtools view -h 17:7512445-7513455

Samtools supports streaming files and piping commands together both using local and remote files. You can get more help with samtools from the samtools help mailing list

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