Links

Is the data for the pilot study still available?

Answer:

All the pilot data remains on our ftp site under the pilot_data directory EBI/NCBI. The variants which are discussed in the pilot paper can also be found on the ftp site EBI/NCBI.

Please note these data are all mapped to the NCBI36 human reference.

Related questions:

How do I get a sub-section of a BAM file?

Answer:

There are two ways to get subsections of our BAM files.

The first is to use the Data Slicer tool from the Ensembl GRCh37 browser which is documented here. This tool gives you a web interface requesting the URL of any BAM file and the genomic location you wish to get a sub-slice for. This tool also works for VCF files.

The second it to use 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

Related questions:

What are CRAM files?

Answer:

CRAM files are alignment files like BAM files. They represent a compressed version of the alignment. This compression is driven by the reference the sequence data is aligned to.

The 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 cram developers mailing list where the format 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.

Related questions:

What are the unmapped bams?

Answer:

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

Related questions:

What is a bas file?

Answer:

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.

Related questions:

What is the difference between the sequence.index and the analysis.sequence.index?

Answer:

The sequence.index file contains a list of all the sequence data produced by the project, pointers to the file locations on the ftp site and also all the meta data associated with each sequencing run.

For the phase 3 analysis the consortium has decided to only use Illumina platform sequence data with reads of 70 base pairs or longer. The analysis.sequence.index file contains only the active runs which match this criterion. There are withdrawn runs in this index. These runs are withdrawn because either: * They have insufficient raw sequence to meet our 3x non duplicated aligned coverage criteria for low coverage alignments. * After the alignment has been run they have failed our post alignment quality controls for short indels. * Contamination. * They do not meet our coverage criteria.

Since the alignment release based on 20120522, we have only released alignments based on the analysis.sequence.index

Related questions:

Where are your alignment files located?

Answer:

Our main alignment files are located in our data directory. Our mapped bams contain reads which aligned to the whole genome.

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.

We also have frozen versions of the alignments use for both the pilot and the phase 1 analyses in different directories on the ftp site. Please note the that the pilot alignments are mapped to NCBI36 rather than GRCh37 like all other alignments on the ftp site.

Related questions:

Why are there chr 11 and chr 20 alignment files, and not for other chromosomes?

Answer:

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.

Related questions: