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