---
title: "08-WGS"
output: html_document
---


```{bash}

for file in ../data/mapped_gigas_WGS/*bam
  do
  sample="$(basename -a $file | cut -d "." -f 1)"
    echo ${sample}
    /home/shared/bedtools2/bin/bedtools coverage \
    -mean \
    -sorted \
    -a ../data/busco-single-copy.bed \
    -b ../data/mapped_gigas_WGS/${sample}.bam \
    > ../analyses/${sample}_bsc_cov.out
done

```

