SexChecker

Check sex of samples using BAM files, k-means clustering, and the number of reads in the sex chromosomes of samples.

Input command line arguments

1. --samplesDir Path to a directory containing BAM files of all samples or subdirectories of the BAM files.
   
2. --cores Number of cores to use for multiprocessing. Default is 1.
   
3. --sampleInfo Path to a sample info .csv file. Must contain Name and Sex columns for each sample.

Algorithm

1. Calculate sex chromosome ratios for each sample.
   
   
   
   
2. For k-means clustering, k = 2 to represent the male and female sexes. All sex chromosome read ratios are divided into two clusters.

• If the value of one cluster center is greater than two the value of the second cluster center, then both male and female samples exist. The sex of samples will be predicted as M or F.
• Otherwise, the sex prediction will be recorded as all M or all F.
  

Output

If there is a mismatch between the predicted sex of a sample and its recorded sex in the sample info file, the Mismatch column in the output file will record Mismatch. Otherwise, if the predicted sex is the same as the sample info sex, a single period . will be recorded in the Mismatch column.

1. sex_checker_[current date and time].print Stores all print statements.
2. sex_checker_output_[current date and time].txt Output of sex checker in tab-delimited format.

Example of output file

Sample_name	ChrX_reads	ChrY_reads	ChrY:ChrX_ratio	ChrY:ChrX_percent	Predicted_sex	Sample_info_sex	Mismatch
Sample_1	4890507	20417	0.004174823	0.41748	F	F	.
Sample_2	5550573	24946	0.004494311	0.44943	F	M	Mismatch
Sample_3	2990996	356739	0.119270972	11.9271	M	M	.