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Standard operating procedure - Alignment, variant calling, and annotation of trio whole exome samples at the Edinburgh Parallel Computing Centre
This SOP applies to batches of family/trio samples where trio whole exome sequencing has been performed by Edinburgh Genomics (EdGE) or the Edinburgh Clinical Research Facility (ECRF). It assumes that data has been successfully transferred to the Edinburgh Parallel Computing Centre (EPCC) (see SOP: Transfer of whole exome sequencing samples from Edinburgh Genomics to Edinburgh Parallel Computing Centre). Scripts are version controlled on the University of Edinburgh gitlab server gitlab.ecdf.ed.ac.uk/igmmbioinformatics/trio-whole-exome. Request access by e-mail: alison.meynert@igmm.ed.ac.uk.
Definitions
In this document, N is the total number of samples in the project, and X is the number of families.
Text in angle brackets, e.g. <project> indicates variable parameters. A variable parameter such as <family1-X> indicates that there are X instances of the parameter, each with their own unique value.
Software and data requirements
The analysis is run with the bcbio pipeline (version 1.2.8) located at /home/u035/u035/shared/software/bcbio. All genome reference and annotation data resources are contained within the genomes/Hsapiens/hg38 subfolder.
The TWIST target BED file is at: /home/u035/u035/shared/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed. See resources.