@groovy.util.logging.Log class SexKaryotyper extends java.lang.Object implements java.lang.Runnable
An algorithm based on simple heuristics for estimating the sex of a sample from sequencing coverage.
| Modifiers | Name | Description |
|---|---|---|
class |
SexKaryotyper.1 |
| Constructor and description |
|---|
SexKaryotyper
(SAM bam, Regions regions) |
| Type Params | Return Type | Name and description |
|---|---|---|
|
IntegerStats |
calcCovStats(Regions regions) |
|
static void |
main(java.lang.String[] args) |
|
void |
run()The primary logic is simply that lack of coverage of the Y chromosome indicates a female sample. |
| Methods inherited from class | Name |
|---|---|
class java.lang.Object |
java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll() |
The primary logic is simply that lack of coverage of the Y chromosome indicates a female sample. So mean coverage < 5x indicates female. In a simple world, we would end with that and conclude that otherwise the sample is male. There are two things that could go wrong, however: we could have very low coverage overall and thus a male with < 5x, or we could have very high coverage overall and thus a female manages to get > 5x coverage even though she has no Y chromosome. The remaining logic protects against these scenarios - first, we only classify a female based on chrY coverage if we have at least 30x mean coverage overall. If we have less than that, or if there is coverage on the Y chromsome, we then look at the ratio of the X chromosome coverage and the autosomes. For a male, we expect it to be about half, while for a female we expect it to be about 1. The 0.7 is simply picking a mid point inbetween those. Note: chr1 and chr22 are used to generate robust estimates of the mean coverage over the autosomes and use that as an estimate of the expected coverage on the X chromosome for females. It's worth noting that in Nextera captures, the chrY coverage appears to be artificially boosted - it comes out about the same as autosome coverage even though there is only theoretically 1 copy. For this reason the absolute value of chrY coverage is not compared to autosome coverage in the logic above.
Groovy Documentation