export PATH=/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/danpos-2.0.0/danpos.py D3.2x36mers.hg38.unique.dedup.filtered.bam,B22.2x36mers.hg38.unique.dedup.filtered.bam,WT.2x36mers.hg38.unique.dedup.filtered.bam,D3.2x36mers.hg38.unique.dedup.filtered.bam-WT.2x36mers.hg38.unique.dedup.filtered.bam,B22.2x36mers.hg38.unique.dedup.filtered.bam-WT.2x36mers.hg38.unique.dedup.filtered.bam,D3.2x36mers.hg38.unique.dedup.filtered.bam-B22.2x36mers.hg38.unique.dedup.filtered.bam --paired 1 -o danpos-2.0.0-all-vs-all-filtered
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/danpos-2.0.0/danpos.py D3.2x36mers.hg38.unique.dedup.filtered.bam-WT.2x36mers.hg38.unique.dedup.filtered.bam --paired 1 -o danpos-2.0.0-D3-vs-WT-filtered
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/danpos-2.0.0/danpos.py B22.2x36mers.hg38.unique.dedup.filtered.bam-B22.2x36mers.hg38.unique.dedup.filtered.bam --paired 1 -o danpos-2.0.0-D3-vs-B22-filtered
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/danpos-2.0.0/danpos.py B22.2x36mers.hg38.unique.dedup.filtered.bam-WT.2x36mers.hg38.unique.dedup.filtered.bam --paired 1 -o danpos-2.0.0-B22-vs-WT-filtered