bio-workflows-cnv-pipeline

Access regions (off-target for WGS-like sensitivity)

cnvkit.py access genome.fa
-o access.bed

cnvkit.py antitarget targets.bed
--access access.bed
-o antitargets.bed

## For each sample

for bam in *.bam; do
    sample=$(basename $bam .bam)

    # Target coverage
    cnvkit.py coverage $bam targets.bed \
        -o coverage/${sample}.targetcoverage.cnn

    # Antitarget coverage
    cnvkit.py coverage $bam antitargets.bed \
        -o coverage/${sample}.antitargetcoverage.cnn
done

From normal samples

cnvkit.py reference
coverage/normal*.targetcoverage.cnn
coverage/normal*.antitargetcoverage.cnn
--fasta genome.fa
-o reference.cnn