Computational protocol: The Anatomy to Genomics (ATG) Start Genetics medical school initiative: incorporating exome sequencing data from cadavers used for Anatomy instruction into the first year curriculum

Similar protocols

Protocol publication

[…] Exome library preparation was performed using the Human Exome Agilent v5 51Mbp (hEx-AV5) kit (Otogenetics, AL). DNA was sequenced on a HiSeq 2500 after exome capture using paired end reads of 100–125 bp with a designated average coverage of 30x or ~2.7-3 Gb. The data were then processed using the DNANexus platform consisting of BWA mapping + GATK SNP/Indel pipeline including mapping with BWA against human reference genome hg19/GRCh37, removing duplicates with Picard MarkDuplicates, realigning the mapped reads using GATK (2.3.9) with information of known indels from dbSNP and the 1000 Genomes project, recalibrating the base quality with GATK, and calling variants with GATK unifiedgenotyper followed by snpEff annotation. SNVs were computationally filtered for those classified as deleterious using the SIFT (Sorting Intolerant From Tolerant) tool [] and/or those with a ClinVar clinical significance annotation [] and included small insertions/deletions. […]

Pipeline specifications

Software tools DNAnexus, BWA, GATK, Picard, SnpEff, SIFT
Applications Miscellaneous, WES analysis
Chemicals Nucleotides