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Naive-RoH

Calculate homozygosity in overlapping windows, from a vcf/bcf file. There exist some very clever ways to identify runs of homozygosity (e.g. using a hidden Markov model), however the code here takes a naive approach---it merely counts homozygous and heterozygous sites in the window based on the genotype call (FORMAT/GT field).

Two components are provided here, (1) a C program, hom_windows, which prints counts of homozygous sites within windows, and (2) a script plot_hom_windows.py that produces a pdf figure of the homozygosity along a chromosome.

Prerequisites

hom_windows uses htslib to parse vcf/bcf files. The plotting script requires python (tested with version 2.7.14 and 3.6.1) and matplotlib (tested with version 2.1.0).

Installation

Clone the git repository, then build with make.

Usage

The recommended way to use hom_windows is to first split your vcf by chromosome and it run separately on each chromosome file. E.g. to split the file infile.vcf.gz by chromosome (for an organism with 26 autosomes), then run hom_windows and plot the result:

for c in $(seq 26) X; do
	chr="chr$c"
	bcftools view -O z -o ${chr}.vcf.gz -r ${chr} infile.vcf.gz
	hom_windows ${chr}.vcf.gz > hom_windows.${chr}.txt
	plot_hom_windows.py --title $chr -o $chr.pdf hom_windows.${chr}.txt
done

Additional control over the window size and the step size for moving along chromosomes can be obtained via command line parameters to hom_windows:

hom_windows v1
usage: ./hom_windows [...] file.vcf

  -s INT         Move window along chromosomes in steps of INT bp [200000].
  -w INT         Output windows of size INT bp [5000000].
  -S STR[,...]   For a multi-sample vcf, specify the sample to use [].
                 Multiple samples may be specified, separated with a comma,
                 in which case loci not segregating among the samples are
                 counted as homozygous.
  -h INT[,...]   Ignore sites with depth higher than INT [1000].
                 If multiple samples are specified, comma separated max depths
                 must be specified for each sample.
  -l INT[,...]   Ignore sites with depth lower than INT [0].
                 If multiple samples are specified, comma separated min depths
                 must be specified for each sample.

The homozygosity from multiple individuals may be included in the same figure by specifying multiple input files and labels for the figure legend.

plot_hom_windows.py \
	--title "Homozygosity along chr1" \
	-o chr1.pdf \
	-l "Individual 1,Individual 2 (inbred line)" \
	hom_windows.ind1.chr1.txt \
	hom_windows.ind2-inbred.chr1.txt

Further control over the scale and aspect ratio of the figure can obtained via command line parameters to the script.

usage: plot_hom_windows.py [-h] [--wide] [--scale SCALE] [--title TITLE]
                           [-o OPDF] [-l LABELS]
                           infiles [infiles ...]

plot `hom_windows' output

positional arguments:
  infiles               input file

optional arguments:
  -h, --help            show this help message and exit
  --wide                plot widescreen ratio (16x9) [False]
  --scale SCALE         scale the plot [1.0]
  --title TITLE         plot title
  -o OPDF, --opdf OPDF  output filename [out.pdf]
  -l LABELS, --labels LABELS
                        comma separated list of labels to correspond with
                        input files