Determine sex from Bam file

Determine sex in Homo sapiens sample from sorted bam file fastly using a simple python script.

Dec 2023 - new version

Key Changes:

• Error Handling: Added more detailed error handling and messages.
• Parameterization of Filters: Users can now pass a comma-separated list of filters as a second argument. If no filters are provided, a default list is used.
• Flexibility in Reference Genome: The script now handles different chromosome naming conventions by checking if chromosome names are numeric for autosomes and looking for 'Y' in the chromosome name for Y chromosome reads.
• Sex Determination Using X/Y Coverage Ratio: The calculate_sex function now calculates the sum of reads for the X chromosome and the Y chromosome separately. It then computes the ratio of X to Y coverage. If this ratio is greater than 4, it classifies the sample as female; otherwise, it classifies it as male.
• Handling Zero Y Reads: To avoid division by zero, if the Y reads are zero, the function automatically classifies the sample as female.

Usage:

python determineSexFromBam.py [bam_file] [optional: filters]

Component required:

1. Samtools
2. Pandas

Installation component required:

conda install -c bioconda samtools
pip install pandas

Output:

Sample	Sex
190106	MALE
191093	MALE
193012	FEMALE
182151	FEMALE
190169	MALE
190210	FEMALE

Licence

MIT LICENCE

Author info

Sr Bioinfo Scientist Adriano De Marino, PhD

Contact: [email protected]