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The Complete Genomics confusion matrix rates. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3338 348d0f76-0448-11de-a6fe-93d51630548a
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kiran 2010-05-10 14:52:10 +00:00
parent b223b04331
commit ec543b7b62
1 changed files with 22 additions and 0 deletions
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22
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionProbabilities.java
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@ -19,6 +19,7 @@ public class EmpiricalSubstitutionProbabilities extends FourBaseProbabilities {
SOLEXA, // Solexa / Illumina
ROCHE454, // 454
SOLID, // SOLiD
CG, // Complete Genomics
UNKNOWN // No idea -- defaulting to 1/3
}
@ -37,6 +38,7 @@ public class EmpiricalSubstitutionProbabilities extends FourBaseProbabilities {
bind("454", SequencerPlatform.ROCHE454);
bind("ILLUMINA", SequencerPlatform.SOLEXA);
bind("solid", SequencerPlatform.SOLID);
bind("CG", SequencerPlatform.CG);
}
public static SequencerPlatform standardizeSequencerPlatform( final String sequencerString ) {
@ -160,6 +162,25 @@ public class EmpiricalSubstitutionProbabilities extends FourBaseProbabilities {
addMisCall(pl, 'T', 'G', 18.5/100.0);
}
private static void addCG() {
SequencerPlatform pl = SequencerPlatform.CG;
addMisCall(pl, 'A', 'C', 28.2/100.0);
addMisCall(pl, 'A', 'G', 28.7/100.0);
addMisCall(pl, 'A', 'T', 43.1/100.0);
addMisCall(pl, 'C', 'A', 29.8/100.0);
addMisCall(pl, 'C', 'G', 18.6/100.0);
addMisCall(pl, 'C', 'T', 51.6/100.0);
addMisCall(pl, 'G', 'A', 32.5/100.0);
addMisCall(pl, 'G', 'C', 21.4/100.0);
addMisCall(pl, 'G', 'T', 46.1/100.0);
addMisCall(pl, 'T', 'A', 42.6/100.0);
addMisCall(pl, 'T', 'C', 34.1/100.0);
addMisCall(pl, 'T', 'G', 23.3/100.0);
}
private static void addUnknown() {
SequencerPlatform pl = SequencerPlatform.UNKNOWN;
for ( char b1 : BaseUtils.BASES ) {
@ -175,6 +196,7 @@ public class EmpiricalSubstitutionProbabilities extends FourBaseProbabilities {
addSolexa();
add454();
addSOLiD();
addCG();
addUnknown();
}