• akrishna_bashrc - contains the .bashrc and .bash_profile for user akrishna
• bam - contains scripts for creating BAM files for regions inside genes
• genome - contains the scripts for the genome sequence workflow
• transcriptome - contains the scripts for the transcriptome sequence workflow

1. CNV annotation
2. HotNet2 - using MutSig scores and [mutations] (genome/variants2/hotnet2/matrix/mutation/)
3. Hotspot analysis
4. SNV density and hom-het ratio for Circos/POMO
5. DNA/RNA SNV comparison
6. Somatic indels - filtering based on frequency and amino-acid changing indels

Data (external databases), Analysis (output files), Tools (3rd party tools) See wiki for further details.