UC Davis Bioinformatics Core 2018 Variant Analysis Workshop
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Software List used in this
General
SLURM
modules
Preprocessing
HTStream github
Alignment
BWA
SAMtools
Variant Calling
Freebayes
DELLY
Picard
GATK
Variant Effect Calling
BEDtools
snpEff
R, Studio, and R packages used
R
RStudio
IdeoViz Package
RCircos Package
devtools Package
qqman Package