zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

A change to the definition of CpG sites (is now, from 5' to 3' a CG dinucleotide in the reference, and the CpG site is at the C, rather than either at the C or a G). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5373 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-03-04 15:36:07 +00:00
parent 9ca1dd5d62
commit 1861ca90fc
2 changed files with 10 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
View File

@ -32,7 +32,8 @@ public class CpG extends VariantStratifier {
String leftFlank = fwRefBases.substring((fwRefBases.length()/2) - 1, (fwRefBases.length()/2) + 1);
String rightFlank = fwRefBases.substring((fwRefBases.length()/2), (fwRefBases.length()/2) + 2);
if (leftFlank.equalsIgnoreCase("CG") || leftFlank.equalsIgnoreCase("GC") || rightFlank.equalsIgnoreCase("CG") || rightFlank.equalsIgnoreCase("GC")) {
//if (leftFlank.equalsIgnoreCase("CG") || leftFlank.equalsIgnoreCase("GC") || rightFlank.equalsIgnoreCase("CG") || rightFlank.equalsIgnoreCase("GC")) {
if (rightFlank.equalsIgnoreCase("CG")) {
isCpG = true;
}
}

16
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -334,7 +334,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String extraArgs = "-L 1:1-10,000,000";
for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
1, Arrays.asList("b1cace2d6c5932a9a85f41fc10e607b4"));
1, Arrays.asList("4ae87d76a3b39cf0b80221f3bd681839"));
executeTestParallel("testSelect1", spec);
//executeTest("testSelect1", spec);
}
@ -365,8 +365,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testVESimple() {
HashMap<String, String> expectations = new HashMap<String, String>();
expectations.put("-L 1:1-10,000,000 -ST CpG", "2a93c62ed4e062c043b7cc6dd0fa55f9");
expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "aade8425705c8870adb9d3fd67cae555");
expectations.put("-L 1:1-10,000,000 -ST CpG", "b82f1ad442d354a5ed3c18ecef93553e");
expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "dc3d34f5a03890217d1f548027a82028");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
@ -389,9 +389,9 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
expectations.put("", "fc552fc9a02ac0d2327d73c375aab45e");
expectations.put(" -knownName comp_hapmap -knownName dbsnp", "09496523136290628bdc233f03ac9a38");
expectations.put(" -knownName comp_hapmap", "8ad493a6427673ca6835303b41f40897");
expectations.put("", "c3936ef2e7af52019ade05461fbf4180");
expectations.put(" -knownName comp_hapmap -knownName dbsnp", "e19bd1bc89463e558fa3b83e65f55ca5");
expectations.put(" -knownName comp_hapmap", "831d69ec830836f7d2ac8310713f1691");
for (String tests : testsEnumerations) {
for (Map.Entry<String, String> entry : expectations.entrySet()) {
String extraArgs2 = entry.getKey();
@ -409,7 +409,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("e83edc273504f5ea11de329f81af3de6"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("132e0825d1ed6e54963da94784cf7803"));
executeTestParallel("testCompVsEvalAC",spec);
//executeTest("testCompVsEvalAC",spec);
}
@ -421,7 +421,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testTranches() {
String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("b018ca01b374def71fcd1bf164326485"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("4c5ef7c142427a85d1b9b1c9fe8fd3c2"));
executeTestParallel("testTranches",spec);
//executeTest("testTranches",spec);
}