对bam按深度进行抽样

1. bam文件平均深度计算

samtools depth -r chr20 ${INPUT_DIR}/HG002_guppy422_2_GRCh38_no_alt.bam | awk '{sum+=$3} END { print "Average Coverage= ",sum/NR}'
# Expected OUTPUT:
# Average Coverage=  50.7078

2. 按照平均深度对bam文件进行向下抽样

for coverage in 30 40 50
do
  total_coverage=51
  downsample_fraction=0.$((coverage * 100 / total_coverage))
  echo "Coverage= ${coverage}, Downsample fraction = ${downsample_fraction}"

  samtools view -s $downsample_fraction -b -@${THREADS} ${INPUT_DIR}/HG002_guppy422_2_GRCh38_no_alt.bam > ${INPUT_DIR}/HG002_guppy422_2_GRCh38_no_alt.${coverage}x.bam
  samtools index -@${THREADS} ${INPUT_DIR}/HG002_guppy422_2_GRCh38_no_alt.${coverage}x.bam
done

这里需要主要 downsample_fraction如果是小于0.1，例如0.05，需要测试，看是否是符合真正的比例