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.

What data do you have?

• Are there any genomic regions that have not been studied?
• Can I get phased genotypes and haplotypes for the individual genomes?
• Can I get phenotype, gender and family relationship information for the individuals?
• Can I query IGSR programmatically?
• Do you have any ancient or prehistoric genomes?
• Do you have assembled FASTA sequences for samples?
• Do you have structural variation data?
• Have you calculated linkage disequilibrium from these variants?
• How were the populations defined?
• Is there gene expression and/or functional annotation available for the samples?
• What types of genotyping data do you have?
• Where were the sampling locations?

What data format?

• About FASTQ sequence read files
• About VCF variant files
• About alignment files (BAM and CRAM)
• About index files
• About variant identifiers
• How are allele frequencies calculated?
• Where can I find a list of the sequencing and analysis done for each individual?

How did you process the data?

• Are the variant calls in IGSR phased?
• How was exome and exon targetted sequencing used?
• How was imputation used in 1000 Genomes to fill in gaps in sequencing?
• Was HLA Diversity studied in IGSR?
• Were the same analysis tools used for every sample in one data collection?
• What is the coverage depth?
• What methods were used for generating alignments?
• What sequencing platforms and methods were used by different projects within IGSR?
• What was the source of the DNA for sequencing?
• Which populations are part of your study?
• Which reference assembly do you use?
• Why are there chr 11 and chr 20 alignment files, and not for other chromosomes?
• Why are there differences between the different analyses of the 1000 Genomes samples?

Working with the data

• Can I get cell lines for IGSR samples?
• Can I map your variant coordinates between different genome assemblies?
• Can I use the IGSR data for imputation?
• Do I need a password to access IGSR data?
• Do I need permission to use IGSR data in my own scientific research?
• How do I cite IGSR?
• How do I find out about new releases?
• Is there any fee associated with using and/or reproducing the data?

My data vs 1000 Genomes Project

• Can I volunteer to be part of the 1000 genomes project?
• Help me to interpret or understand more about a genetic disease diagnosis.
• Help me to interpret or understand more about my personal genomics data.
• How do I contact one of the individuals whose genome you have sampled?

How to get the data?

• Are the IGSR variants available in dbSNP?
• Are the IGSR variants available in genome browsers?
• Can I BLAST against the sequences in IGSR?
• Can I convert VCF files to PLINK/PED format?
• Can I search the website?
• How can I get VCFs of a single population or individual?
• How can I get all variants in a particular gene?
• How can I get gene sequences for individuals?
• How do I find out information about a single variant?
• How do I find specific alignment files?
• How do I find specific sequence read files?
• How do I find specific variant files?
• How do I find the most up-to-date data?
• How do I find the reference genomes files?
• How do I get a genomic region sub-section of your files?
• What tools can I use to download IGSR data?
• Where can I get consequence annotations for the IGSR variants?

Data problems?

• Is the sequencing data in IGSR contaminated with mycoplasma?
• There is a corrupt file on your ftp site.
• Why are the coordinates of some variants different to what is displayed in other databases?
• Why are there duplicate calls in the phase 3 call set?
• Why are there gaps in the X and Y chromosome?
• Why can't I find one of your variants in another database?
• Why do some of your vcf genotype files have genotypes of ./. in them?
• Why does a tabix fetch fail?
• Why is the allele frequency different from allele count/allele number?

About

• Are there any statistics about how much sequence data is in IGSR?
• Do you have any job vacancies?
• Does the 1000 Genomes Project use HapMap data?
• How do I contact you?
• How do I find the familial relationships between the individuals?
• How do I navigate the FTP site to find the files I need?
• How many individuals have been sequenced in IGSR projects and how were they selected?
• What are the different data collections available for 1000 Genomes?
• What are your filename conventions?
• What do the population codes mean?
• Which datasets include related individuals?