diff --git a/codes/qc_stat.py b/codes/qc_stat.py index 42bf6a3..7452285 100755 --- a/codes/qc_stat.py +++ b/codes/qc_stat.py @@ -52,6 +52,7 @@ with open(os.path.join(bamdst_out, 'coverage.report'), 'r') as file2: out.write(''.join(["mean_depth(dedup)\t", str(bamdst["[Target] Average depth(rmdup)"]), "\n"])) out.write(''.join(["coverage(>0x)\t", str(bamdst["[Target] Coverage (>0x)"].replace('%', '')), "\n"])) out.write(''.join(["coverage(>10x)\t", str(bamdst["[Target] Coverage (>=10x)"].replace('%', '')), "\n"])) + out.write(''.join(["coverage(>30x)\t", str(bamdst["[Target] Coverage (>=30x)"].replace('%', '')), "\n"])) uniformity = round((float(bamdst["[Target] Average depth"])) * 0.2) b = os.popen("sed -n %s'p' %s | cut -f5" % (uniformity, os.path.join(bamdst_out, 'depth_distribution.plot')))