All our alignment files are in BAM or CRAM format. BAM is a standard alignment format which was defined by the 1000 Genomes consortium and has since seen wide community adoption, whereas CRAM is a compressed version of this. This compression is driven by the reference the sequence data is aligned to.
The CRAM file format was designed by the EBI to reduce the disk footprint of alignment data in these days of ever-increasing data volumes.
The CRAM files the 1000 Genomes project distributes are lossy cram files which reduce the base quality scores using the Illumina 8-bin compression scheme as described in the lossy compression section on the cram usage page
There is a github page where the format of CRAM file is discussed and help can be found.
CRAM files can be read using many Picard tools and work is being done to ensure samtools can also read the file format natively.
The bam file names look like:
NA00000.location.platform.population.analysis_group.YYYYMMDD.bam
The bai index and bas statistics files are also named in the same way.
The name includes the individual sample ID, where the sequence is mapped to, if the file has only contains mapping to a particular chromosome that is what the name contains otherwise, mapped means the whole genome mapping and unmapped means the reads which failed to map to the reference (pairs where one mate mapped and the other didn’t stay in the mapped file), the sequencing platform, the ethnicity of the sample using our three letter population code, the sequencing strategy. The date matches the date of the sequence used to build the bams and can also be found in the sequence.index filename.
The unmapped bams contain all the reads for the given individual which could not be placed on the reference genome. It contains no mapping information
Please note that any paired end sequence where one end successfully maps but the other does not both reads are found in the mapped bam
Bas files are statistics we generate for our alignment files which we distribute alongside our alignment files.
These are readgroup level statistics in a tab delimited manner and are described in this README
Each mapped and unmapped bam file has an associated bas file and we provide them collected together into a single file in the alignment_indices directory, dated to match the alignment release.
Our data is in standard formats like SAM and VCF, which have tools associated with them. To manipulate SAM/BAM files look at SAMtools for a C based toolkit and links to APIs in other languages. To interact with VCF files look at VCFtools which is a set of Perl and C++ code.
The easiest way to find the alignment files you’re looking for is with the Data Portal. You can search for individuals, populations and data collections, and filter the files by data type and technologies. This will give you locations of the files, which you can use to download directly, or to export a list to use with a download manager.
You can find an index of our alignments in our alignment.index file. There are dated versions of these files and statistics surrounding each alignment release in the alignment_indicies directory. Please note with few exceptions we only keep the most recent QC passed alignment for each sample on the ftp site.
The easiest way to find the sequence files you’re looking for is with the Data Portal. You can search for individuals, populations and data collections, and filter the files by data type and technologies. This will give you locations of the files, which you can use to download directly, or to export a list to use with a download manager.
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 ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz 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 ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz chr2:39967768-39967768
You can subset alignment files with samtools on the command line, e.g.
samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam 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
Details of alignment methodology differ between data sets and the types of sequence data being aligned.
Full details of methodology can be found in the publications accompanying the data collections and, for unpublished alignments, in the README files placed with the data collections on our FTP site.
The chr 11 and chr 20 alignment files are put in place to give the 1000 Genomes analysis group a small section of the genome to run test analyses on before committing to a particular strategy to run across the whole genome. Everything in the chr 11 and chr 20 files is also represented in the mapped bam file. To get a complete view of what data we aligned you only need to download the mapped and unmapped bams, the chr 11 and chr 20 bams are there as a convenience to the analysis group.