IGSR: The International Genome Sample Resource

FAQ

This is the FAQ from the 1000 Genomes Project. This list of questions is not exhaustive. If you have any other questions you can’t find the answer to please email info@1000genomes.org to ask.

• Are all the genotype calls in the 1000 Genomes Project current release VCF files bi-allelic?
• Are all the variants displayed on the 1000 Genomes Project Browser discovered by the project?
• Are the 1000 genomes variant calls phased?
• Are the 1000 genomes variants in dbSNP?
• Are there any FASTA files containing 1000 Genomes variants or haplotypes?
• Are there any assemblies available for the 1000 Genomes samples?
• Are there any scripts or APIs for use with the 1000 Genomes data sets?
• Are there any statistics about how much sequence data has been generated by the 1000 Genomes Project?
• Are there torrents available for the 1000 Genomes data sets?
• Can I BLAST against the 1000 Genomes data sets?
• Can I access 1000 Genomes data with Globus Online?
• Can I access the databases associated with the 1000 Genomes browser?
• Can I convert VCF files to PLINK/PED format?
• Can I find the genomic position for a list of dbSNP rs numbers?
• Can I get 1000 Genomes data on the Amazon Cloud?
• Can I get cell lines for 1000 Genomes Samples?
• Can I get genotypes for a specific individual/population from VCF files?
• Can I get haplotype data for the 1000 Genomes individuals?
• Can I get image files for any of the 1000 Genomes sequencing runs?
• Can I get individual genotype information from browser.1000genomes.org?
• Can I get phenotype, gender and family relationship information for the 1000 Genomes samples?
• Can I map your variant coordinates between different genome assemblies?
• Can I search the website?
• Can I use the 1000 genomes data for imputation?
• Can I volunteer to be part of the 1000 genomes project?
• Do I need a password to access 1000 genomes data?
• Do I need permission to use the 1000 Genomes data in my own scientific research?
• Does the 1000 Genomes Project use HapMap data?
• How are your alignments generated?
• How can I get the allele frequency of my variant?
• How do I cite IGSR?
• How do I cite the 1000 genomes project?
• How do I contact you?
• How do I find out about new 1000 genomes releases?
• How do I get a sub-section of a BAM file?
• How do I get a sub-section of a VCF file?
• How does an individual have a genotype in a location where it has no sequence coverage?
• How many individuals were sequenced?
• How much sequence data has been generated for single individuals?
• How to download ENA files using aspera?
• How to download files using aspera?
• Is the 1000 Genomes sequencing data contaminated with mycoplasma?
• Is the 1000 genomes data available in genome browsers?
• Is the data for the pilot study still available?
• Is there any functional annotation for the 1000 Genomes phase 1 data?
• Is there any gene expression data available for the 1000 Genomes Project samples?
• There is a corrupt file on your ftp site.
• What Affy 6.0 genotype data do you have?
• What Axiom genotype data do you have?
• What High Density Genotyping information do you have?
• What Omni genotype data do you have?
• What Sequencing Platforms were used for the 1000 Genomes Project?
• What are CRAM files?
• What are the kgp identifiers?
• What are the targets for your exon targetted pilot study?
• What are the targets for your whole exome sequencing?
• What are the unmapped bams?
• What are your filename conventions?
• What capture technology did the Exome sequencing use?
• What do the names of your fastq files mean?
• What do the names of your variant files mean and what format are the files?
• What do the pilot project, phase 1, phase 2 and phase 3 mean?
• What do your population codes like CEU or TSI mean?
• What does Genotype Dosage mean in the phase 1 integrated call set?
• What does the LDAF value mean in your phase1 VCF files?
• What does this variant identifier mean?
• What format are your alignments in and what do the names mean?
• What format are your sequence files?
• What is a bas file?
• What is a panel file?
• What is a sequence index file?
• What is the Data Slicer?
• What is the HLA Diversity in 1000 Genomes Samples?
• What is the depth of coverage of your Phase1 variants?
• What is the difference between the analysis groups exome and exon targetted in the sequence index?
• What is the difference between the sequence.index and the analysis.sequence.index?
• What is the difference between your data directory and the pilot_data/data directory?
• What library insert sizes where used in the 1000 genomes project?
• What percentage of the genome is assayable?
• What read lengths were used by the project?
• What strand are the variants in your VCF file on?
• What structural variant data is available for the project?
• What tools can I use to download 1000 Genomes data?
• What version of VCF are your VCF files in?
• What was the source of the DNA for sequencing?
• Where are the SNPs for the X/Y/Mitochondrial chr?
• Where are the alignment files for the exon targetted individuals?
• Where are the pilot structural variants archived?
• Where are your alignment files located?
• Where are your reference data sets?
• Where are your sequence files located?
• Where are your variant files located?
• Where can I find phase3 alignment BAM files and read fastq files on the ftp site?
• Where can I get consequence annotations for the 1000 genome variants?
• Where does the Ancestral Allele Information for your variants come from?
• Where is the most recent release?
• Which of your phase1 variant sites have imputed genotypes?
• Which populations are part of your study?
• Which reference assembly do you use?
• Which samples are you sequencing?
• Why are phase 1 sites missing from the phase 3 dataset?
• Why are the coordinates of your pilot variants different to what is displayed in Ensembl or UCSC?
• Why are there chr 11 and chr 20 alignment files, and not for other chromosomes?
• Why are there duplicate calls in the phase 3 call set
• Why are there more than one set of fastq files associated with an individual?
• Why do some of your vcf genotype files have genotypes of ./. in them?
• Why do some variants in the phase1 release have an zero Allele Frequency?
• Why does a tabix fetch fail?
• Why is the allele frequency different from allele count/allele number?
• Why is the sequence data distributed in 2 or 3 files labelled SRR_1, SRR_2 and SRR?
• Why isn’t a SNP in dbSNP or HapMap?
• Why isn’t my SNP in browser.1000genomes.org?