Use BS data (bam) to examine copy number variation

[sr320]

cd /gscratch/scrubbed/sr320/021022-CvBSnp/
FILES=$(ls *sorted.bam)

for file in ${FILES}
do
    NAME=$(echo ${file} | awk -F "." '{print $1}')
    echo ${NAME}

    /gscratch/srlab/programs/bedtools-2.27.1/bin/bedtools coverage \
    -mean \
    -sorted \
    -a /gscratch/srlab/sr320/data/Cvirg-genome/C_virginica-3.0_Gnomon_genes.bed \
    -b /gscratch/scrubbed/sr320/021022-CvBSnp/${NAME}.deduplicated.sorted.bam \
    > ${NAME}_cov_m.out
done

output https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/021722-gen-cov/

[sr320]

next step is get 24 samples files into matrix