Hi everyone,

We did the following:

#!/bin/sh

# This script will create the following files in
# 1. Present Working Directory (PWD):
# - access.hg38.bed
# - antitargets.hg38.bed
# - FlatReference.cnn
#
# 2. /PWD/batch1:
# - BAM_FILE_1.antitargetcoverage.cnn
# - BAM_FILE_1.targetcoverage.cnn
# - BAM_FILE_2.antitargetcoverage.cnn
# - BAM_FILE_2.targetcoverage.cnn
# ...
# - BAM_FILE_N.antitargetcoverage.cnn
# - BAM_FILE_N.targetcoverage.cnn

# Set CORES = to your machine or if less, number of BAM files.
CORES=64

TARGET=/PATH_TO/Exome-Agilent_V6.bed
FASTA=/PATH_TO/hg38.fa
DIR=/PATH_TO/WES/BAM/

cnvkit.py access $FASTA --output access.hg38.bed

cnvkit.py antitarget ${TARGET} \
  --access access.hg38.bed \
  --output antitargets.hg38.bed

cnvkit.py reference \
  --output FlatReference.cnn \
  --fasta $FASTA \
  --targets ${TARGET} \
  --antitargets antitargets.hg38.bed

cnvkit.py batch ${DIR}/*.bam --reference FlatReference.cnn \
            --output-dir batch1 \
            --diagram --scatter -p ${CORES}