This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome
sequencing data to a reference and produce high‐quality variant calls that can be used in …

… Geraldine Van der Auwera, longtime custodian of the GATK user community, and Brian O'Connor
of the UC Santa Cruz Genomics Institute guide you through the process. You'll learn by …

Comprehensive disease gene discovery in both common and rare diseases will require the
efficient and accurate detection of all classes of genetic variation across tens to hundreds of …

… AnVIL Methods Geraldine A Van der Auwera Data Sciences Platform Broad Institute of
MIT and Harvard 415 Main St, Cambridge, MA 02142 Terra Outreach and Communications …

… Van der Auwera, unpublished data). The TRAPPIST toolbox was used to perform multiple
alignments with Mauve, produce refined pairwise alignments between segments using …

Background Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis belong to the
genetically close-knit Bacillus cereus sensu lato group, a family of rod-shaped Gram-positive …

The Bacillus cereus sensu lato group is genetically very close and possesses a remarkable
plasmid gene pool that encodes a variety of functions such as virulence and self-transfer …

… Van der Auwera, Genome Sequencing and Analysis Group, Broad Institute, … Van der Auwera,
Genome Sequencing and Analysis Group, Broad Institute, Cambridge, … Van der Auwera …

… -based sequence map and alignment drawing tool for plasmids (Van der Auwera, in
preparation), with identity scoring by the BLAST algorithm bl2seq (Tatusova and Madden 1999). …

The presence of cytotoxin K (cytK), nonhemolytic (NHE), and hemolytic (HBL) enterotoxin
genes was investigated in 74 Bacillus thuringiensis strains recovered from the intestines of …