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Sequencing Pipelines
Sequencing Data Generation
The three Large Scale Sequencing/Analysis Centers (LSACs) sequencing ADSP data include the Human Genome Sequencing Center at Baylor College of Medicine, Broad Institute, and Genome Institute at Washington University. The three LSACs generated paired-end sequencing BAM files (currently available in dbGaP, phs000572) using the settings below.
BAM files are collected together from dbGaP, then called as project-level VCFs by Broad Institute and Baylor College of Medicine (these are intermediate files and not available to the public). The ADSP Quality Control Work Group combines the two project-level VCF datasets and performs QC and concordance checks into an overall ADSP VCF file.
Sequencing Pipeline Tools and Parameters
| Program | Baylor | Broad | WashU |
|---|---|---|---|
| CASAVA | 1.8.3 | N/A | 1.8.2 |
| Reference | GRCh37-lite | GRCh37 (1kg version) | GRCh37-lite |
| Aligner | BWA 0.6.2 | BWA 0.5.9-tpx | BWA 0.5.9 |
| Aligner Parameters | defaults; -t 8 | defaults; -t N -q 5 | defaults; -t 4 -q 5 |
| Sort/Dupe/Mates | Picard 1.93 | Picard (latest) | Picard 1.46 |
| Merge | Picard 1.41 | Picard (latest) | Picard 1.46 |
| GATK indels | v2.5-2; 1kG, Mills, dbSNP137 | v2.6-14 | v2.4; 1kG, Mills, dbSNP137 |
| GATK recal | v2.5-2 | v2.6-14 | v2.4 |
| ReduceReads | no | yes | no |
Whole-Exome Target Regions
Broad Institute used the Illumina Rapid Capture Exome (ICE) kit, download target regions.
Baylor and WashU used the Nimblegen's VCRome v2.1, download target regions.
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