Data delivery varies depending on the specifics of the project. Factors that influence the type of data returned include species and library construction method.
For Human WGS and Exome Projects:
- bam file (*.bam) – is a binary SAM file that contains the sequence alignment data for a single sample created using BWA
- bam index file (*.bam.bai) – are the index files for the corresponding bam files
- Multi-sample vcf file (.vcf) – contains all samples in a project called at every site that is variant in at least one of the samples as generally recommended by GATK best practices. For more information on VCF format go to: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
- Sample ID Lookup table (.xls) – is a cross-reference between the UW-CMG LIMS IDs generated at the sequencing center and the investigator sample IDs. It also lists the family information for the project.
- Genotype data – Not all projects will have high-density genotyping data generated. If the project was genotyped, the investigator will receive a PLINK-formatted file containing the genotypes. For more information on PLINK, go to: https://zzz.bwh.harvard.edu/plink/tutorial.shtml
*FASTQs can be released for any project type