Sex

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

gngs.tools.Sex

```
@groovy.util.logging.Log
class Sex
extends ToolBase
```
Estimates the sex of a sample from one or more VCF file and prints to the console.
Usage:
```
gngs Sex <vcf file>
```
See gngs.VCF#guessSex(int) for details of how sex is determined.
Authors:
Simon Sadedin

Properties Summary

Properties
Type	Name and description
`static java.lang.String`	`AMELY_BASES`
`static java.lang.Object`	`MALE_AMELY_READ_THRESHOLD`

Constructor Summary

Constructors
Constructor and description
`Sex ()`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`Sex`	`guessFastqSex(java.lang.String fastqPath)`
	`static java.lang.Object`	`main(java.lang.Object args)`
	`java.lang.String`	`processBAM(java.lang.String bamPath)`
	`void`	`processParallelBAMs(java.util.List<java.lang.String> bamFiles)`
	`void`	`run()`

- Property Detail
  - static final java.lang.String AMELY_BASES
  - static final java.lang.Object MALE_AMELY_READ_THRESHOLD
- Constructor Detail
  - Sex()
- Method Detail
  - @groovy.transform.CompileStatic Sex guessFastqSex(java.lang.String fastqPath)
  - static java.lang.Object main(java.lang.Object args)
  - java.lang.String processBAM(java.lang.String bamPath)
  - void processParallelBAMs(java.util.List<java.lang.String> bamFiles)
  - void run()

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation