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| | Deep coverage exome capture sequencing supports reliable discovery |
| | of rare variants, including those which appear only once or twice across |
| | all individuals sequenced. |
| | Exome capture sequencing was performed for 1128 individuals in |
| | HapMap and 1000 Genomes population samples by four sequencing |
| | centers, Beijing Genome Institute, Baylor College of Medicine |
| | Human Genome Sequencing Center, Broad Institute and Washington |
| | University Genome Sequencing Center, using either the NimbleGen |
| | SeqCap_EZ_Exome_v2 (BGI, BCM) or Agilent SureSelect_All_Exon_V2 |
| | (BI, WUGSC) exome capture reagents. All sequencing was done from |
| | lymphoblastoid cell line DNA. Sequencing was considered complete |
| | when at least 70% of the target region showed 20x or greater depth |
| | of coverage in mapped reads. Target regions for analysis are the |
| | intersection of the two capture reagent target regions with CCDS |
| | coding exons, plus 50 bp flanking regions. This totals approximately |
| | 47 Mb, of which 62% are coding exons. Exact boundaries in GRCh37 |
| | sequence coordinates are shown in file: |
| | /ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/ |
| | exome_pull_down_targets/20110426_exome_add50bp.consensus.bed |
| | Illumina sequence reads were mapped at Broad Institute using BWA |
| | and at Boston College using Mosaik. AB SOLiD sequence reads were |
| | mapped at Baylor using Bfast and at Boston College using Mosaik. |
| | All read mapping uses the GRCh version 37 human genome reference |
| | sequence, without additional decoy sequences. The final site list is the |
| | union of calls from both sequencing technologies, separately filtered |
| | using SVM. |
| | While formatting the data for dbSNP submission, I observe that the |
| | single ALT allele shown in the 1000 Genomes Phase 1 integrated |
| | genotypes sometimes differs from that found in the contributing call |
| | sets. For consistency, the allele from the integrated genotypes is |
| | shown here. |
| | Data availability: |
| | The mapped sequence reads are indexed in file: |
| | /ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/alignment_indices/ |
| | 20110521.exome.alignment.index |
| | The original SNP calls from individual centers, the filtered union |
| | site lists and integrated genotypes are currently found in directories: |
| | /ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/technical/working/ |
| | 20110721_exome_call_sets |
| | 20110810_exome_consensus_snps |
| | 20120117_new_phase1_intgrated_genotypes (sic) |
