class VCFSimilarity extends java.lang.Object
A simple measurement of similarity of different samples by counting the number of shared vs different SNVs. This measurement can be used as a simplistic way to detect relatedness among a set of samples that are all sequenced together. For unrelated samples the number of different SNVs will be approximately similar (while still clustering strongly around population). For related samples there will be significantly more shared SNVs and fewer distinct SNVs. This tool does not replace a more formal estimation of relatedness, and no hard conclusions should be drawn from its output. Its main beneifit is that it is very simple and runs very quickly and easily even on a fairly large set of samples, and thus is suitable for use as a QC measure.
| Type | Name and description |
|---|---|
graxxia.Matrix |
nonSelfMeans |
graxxia.Matrix |
onlyCounts |
java.util.Map |
sampleVariantMetrics |
java.util.List<java.lang.String> |
samples |
graxxia.Matrix |
sharedCounts |
java.util.List<java.lang.String> |
vcfFiles |
java.util.List<VCF> |
vcfs |
graxxia.Matrix |
zscores |
| Constructor and description |
|---|
VCFSimilarity
(java.lang.String[] vcfFiles) |
| Type Params | Return Type | Name and description |
|---|---|---|
|
void |
compute() |
|
java.util.Set |
getVariantSet(gngs.VCF vcf, java.lang.String sample) |
|
static void |
main(java.lang.String[] args) |
| 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() |
Groovy Documentation