diploid2haploid.py

The script converts diploid genotypes to haploid genotypes for the sex chromosomes of males in a vcf file. The scripts modifies only GT fields with others remain. Heterozygous genotypes in the sex chromosomes of males, if any, are converted to be missing.

The script was tested in Python 3.7 with the vcf file produced by stacks 2.5.

Dependencies

Python 3

argparse

Inputs

• vcf file
• sex assignment file, which is tab-delimited text file with each line consisting of sample name and sex (female or male), like this:

  lib1_1_A	female
  lib1_1_B	male
  lib1_1_C	female
  lib1_1_D	male
  

  It is required when a input vcf file contains not only males but also females.

Outputs

The script outputs modified vcf file and summary report as follows.

• output.vcf
• output_summary.txt

These are provided in a current directory by default.
Output directory and file name can be changed via -o option.

Usage

usage: diploid2haploid.py [-h] -i INPUT_VCF -y YCHROM -x XCHROM
                          [-o OUTPUT_VCF] [-s SEX]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT_VCF, --input_vcf INPUT_VCF
                        Name of input vcf file
  -y YCHROM, --ychrom YCHROM
                        Name of Y chromosome in reference sequence
  -x XCHROM, --xchrom XCHROM
                        Name of X chromosome in reference sequence
  -o OUTPUT_VCF, --output_vcf OUTPUT_VCF
                        Name of output vcf file. By default, it is
                        ./output.vcf
  -s SEX, --sex SEX     File of sex assignment, required when input vcf file
                        contains females

Examples

./diploid2haploid.py -i input.vcf -y NC_027914.1 -x NC_041774.1

This assumes that all the samples in an input vcf file are males. If an input vcf file contains not only males but also females, use -s option.

Author

ITO Tsuyoshi

License

This project is licensed under the MIT License - see the LICENSE file for details