Determine sex in Homo sapiens sample from sorted bam file fastly using a simple python script.
Dec 2023 - new version
- 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_sexfunction 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.
python determineSexFromBam.py [bam_file] [optional: filters]
conda install -c bioconda samtools
pip install pandas
| Sample | Sex |
|---|---|
| 190106 | MALE |
| 191093 | MALE |
| 193012 | FEMALE |
| 182151 | FEMALE |
| 190169 | MALE |
| 190210 | FEMALE |
Sr Bioinfo Scientist Adriano De Marino, PhD
Contact: adriano.demarino@gmail.com