In the original phase 1 and 3 sequencing of the 1000 Genomes individuals, many genomes were only sequenced in full at low coverage, so some individuals some genotypes will be based on imputation.
This means that if an individual has no coverage at a particular location but overall we have been able to determine there is variation at that location then we can statistically infer the genotype for that variant in that individual using haplotype information. This means we are able to provide complete haplotypes for all the variation we discover.
The process used to create our genotypes first gave our merged sites and genotype likelihoods sets to Beagle to generate initial haplotypes (using 50 interations across all samples) and these were refined using a modified version of Thunder (it used 300 states chosen by longest matching haplotype at each iteration in addition to 100 randomly chosen states).
This process means we are unable to precisely identify which sites used imputation to generate their genotype. Without this process the approximate error rate for our heterozygous sites would be 20% so you can estimate that 20% of our heterozgous sites will have been changed on the basis of imputation. The sites covered by our exome sequencing represent our highest accuracy sites and these are the least likely to have been changed by this process. The converse is also true any site without any sequence alignment will have been imputed. You can find the depth of coverage at any site using our bam files. Other sites may have been given greater evidence on the basis of the imputation and refinement process.
You can find out more about this in our Phase 1 paper.
The Phase 1 integrated variant set does not report the depth of coverage for each individual at each site. We instead report genotype likelihoods and dosage. If you would like to see depth of coverage numbers you will need to calculate them directly.
The bedtools suite provides a method to do this.
genomeCoverageBed is a tool which can provide a bed file which specifies coverage for every base in the genome and intersectBed which will provide an intersection between two vcf/bed/bam files.
These commands also require samtools, tabix and vcftools to be installed.
An example set of commands would be:
samtools view -b ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG01375/alignment/HG01375.mapped.ILLUMINA.bwa.CLM.low_coverage.20120522.bam 2:1,000,000-2,000,000 | genomeCoverageBed -ibam stdin -bg > coverage.bg
This command gives you a bedgraph file of the coverage of the HG01375 bam between 2:1,000,000-2,000,000:
tabix -h http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/ALL.chr2.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz 2:1,000,000-2,000,000 | vcf-subset -c HG01375 | bgzip -c > HG01375.vcf.gz
This command gives you the vcf file for 2:1,000,000-2,000,000 with just the genotypes for HG01375.
To get the coverage for all those sites you would use:
intersectBed -a HG01375.vcf.gz -b coverage.bg -wb > depth_numbers.vcf
You can find more information about bed file formats please see the Ensembl File Formats Help.
For more information you may wish to look at our documentation about data slicing.