faq.md

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single_section	FAQ	/faq/	FAQ	true	/node/503/	How were the populations defined? Where were the sampling locations? Do you have any ancient or prehistoric genomes? Have you calculated linkage disequilibrium from these variants? What are the phases of 1000 Genomes and how do I access the data from them? Do you have assembled FASTA sequences for samples? Can I query IGSR programmatically? Can I get phased genotypes and haplotypes for the individual genomes? Can I get phenotype, gender and family relationship information for the individuals? Is there gene expression and/or functional annotation available for the samples? What types of genotyping data do you have? Are there any genomic regions that have not been studied? Do you have structural variation data?	About VCF variant files About FASTQ sequence read 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?	Why are there chr 11 and chr 20 alignment files, and not for other chromosomes? Were the same analysis tools used for every sample in one data collection? Are the variant calls in IGSR phased? What methods were used for generating alignments? How was imputation used in 1000 Genomes to fill in gaps in sequencing? What sequencing platforms and methods were used by different projects within IGSR? How was exome and exon targetted sequencing used? Was HLA Diversity studied in IGSR? What is the coverage depth? What was the source of the DNA for sequencing? How do you calculated ancestral alleles? Which populations are part of your study? Which reference assembly do you use? Why are there differences between the different analyses of the 1000 Genomes samples?	Is there any fee associated with using and/or reproducing the data? Can I get cell lines for IGSR samples? 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 find out about new releases? Can I map your variant coordinates between different genome assemblies? How do I cite IGSR?	Can I volunteer to be part of the 1000 genomes project? How do I contact one of the individuals whose genome you have sampled? Help me to interpret or understand more about my personal genomics data. Help me to interpret or understand more about a genetic disease diagnosis.	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? Are the IGSR variants available in dbSNP? What tools can I use to download IGSR data? Can I BLAST against the sequences in IGSR? How do I find out information about a single variant? How do I get a genomic region sub-section of your files? Are the IGSR variants available in genome browsers? How do I find specific alignment files? How do I find specific variant files? How do I find specific sequence read files? How do I find the reference genomes files? Where can I get consequence annotations for the IGSR variants? How do I find the most up-to-date data? Can I convert VCF files to PLINK/PED format? Can I search the website?	Why are there gaps in the X and Y chromosome? Is the sequencing data in IGSR contaminated with mycoplasma? 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 is the allele frequency different from allele count/allele number? Why can't I find one of your variants in another database? There is a corrupt file on your ftp site. 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?	How do I find the familial relationships between the individuals? Do you have any job vacancies? Which datasets include related individuals? Does the 1000 Genomes Project use HapMap data? How do I contact you? Are there any statistics about how much sequence data is in IGSR? 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 do the population codes mean? How do I navigate the FTP site to find the files I need? What are your filename conventions?

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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 [email protected] to ask.

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What data do you have?

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What data format?

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How did you process the data?

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Working with the data

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My data vs 1000 Genomes Project

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How to get the data?

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Data problems?

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About

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