exome target coverage: http://www.gettinggeneticsdone.com/2014/03/visualize-coverage-exome-targeted-ngs-bedtools.html

target_cov.sh

#!/bin/bash
#SBATCH -p bcbio
#SBATCH -a 1-60
set -e
source /WORK/app/toolshs/cnmodule.sh
module load bedtools/2.26.0

which bedtools
bedtools --version
## create output dir
[ -d "bedcov" ] || mkdir bedcov

## monitor
collectl -i 5 -c 3600 -scmdn -f ./bedcov &

## Set up to run in GNU parallel.
# find ../out_bcbio/final/ -name "*-ready.bam" | sort | sed -n "$SLURM_ARRAY_TASK_ID, $((SLURM_ARRAY_TASK_ID + 1)) p" | parallel -j 2 'bedtools coverage -hist -sorted -a ../ex_region.sort.bed -b {} | grep ^all > ./bedcov/{/}.hist.all.txt '
# What this actually runs:
# bedtools coverage -hist -a target_regions.bed -b samp.01.bam | grep ^all > samp.01.bam.hist.all.txt
# bedtools coverage -hist -a target_regions.bed -b samp.02.bam | grep ^all > samp.02.bam.hist.all.txt

inbam=`find ../out_bcbio/final/ -name "*-ready.bam" | sort | sed -n "$SLURM_ARRAY_TASK_ID p"`
bedfile="../ex_region.sort.bed"
outtxt="./bedcov/"`basename $inbam`".hist.all.txt"

if [ -f $outtxt.ok ]; then
    echo skip because file exists
else
    echo "bedtools coverage -hist -sorted -g hg19.genomeFile.txt -a ../ex_region.sort.bed -b $inbam | grep '^all' > $outtxt"
    bedtools coverage -hist -sorted -g hg19.genomeFile.txt -a ../ex_region.sort.bed -b $inbam | grep '^all' > $outtxt && touch $outtxt.ok
fi

## stop collectl
kill %1

echo "DONE in $SECONDS seconds"
exit 0