Sina Majidian sinamajidian

Bioinformatician | Postdoctoral Fellow at the Johns Hopkins University | Formerly at University of Lausanne & Wageningen University & Research.

sinamajidian / depth_mean_stddev.py

Created October 10, 2020 07:27 — forked from williamrowell/depth_mean_stddev.py

Calculate the mean and standard deviation of a coverage depth distribution as if it were normally distributed.

	#!/usr/bin/env python3
	"""Coverage mean and standard deviation of autosomes

	Estimate the mean and standard deviation from a mosdepth coverage BED for
	positions with coverage in the range (0, 2 * non-zero mode). This estimate
	behaves well for PacBio HiFi WGS of human germline aligned to either hs37d5 and
	GRCh38, and may be useful for other situations as well.

	$ bash mosdepth --threads 3 --no-per-base --by 500 -m "${BAM%.*}.median" "${BAM}"
	$ tabix ${BAM%.*}.median.regions.bed.gz {1..22} \| python depth_mean_stddev.py