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a) Changed the way we classify and log indel events (e.g. in IndelClasses table inside IndelStatistics VE module). Made names clearer, and split logging of event length with number of repetitions of event. 

b) Add an experimental annotation to log indel type string inside the INFO field, just for debugging/temp analysis purposes (will consider making it standard if it proves useful). 



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5424 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-03-11 17:37:41 +00:00
parent 4a09d25a90
commit b03055099a
2 changed files with 84 additions and 16 deletions
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48
java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java 100755
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@ -0,0 +1,48 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFHeaderLineType;
import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.IndelUtils;
import java.util.*;
/**
* Created by IntelliJ IDEA.
* User: delangel
* Date: Mar 11, 2011
* Time: 11:47:33 AM
* To change this template use File | Settings | File Templates.
*/
public class IndelType implements InfoFieldAnnotation, ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
int run;
if ( vc.isIndel() && vc.isBiallelic() ) {
String type="";
ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
for (int k : inds) {
type = type+ IndelUtils.getIndelClassificationName(k)+".";
}
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%s", type));
return map;
} else {
return null;
}
}
public List<String> getKeyNames() { return Arrays.asList("IndelType"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("IndelType", 1, VCFHeaderLineType.String, "Indel type description")); }
}

52
java/src/org/broadinstitute/sting/utils/IndelUtils.java
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@ -20,7 +20,7 @@ public class IndelUtils {
static {
COLUMN_KEYS= new String[41];
COLUMN_KEYS= new String[51];
COLUMN_KEYS[0] = "Novel_A";
COLUMN_KEYS[1] = "Novel_C";
COLUMN_KEYS[2] = "Novel_G";
@ -51,17 +51,27 @@ public class IndelUtils {
COLUMN_KEYS[27] = "RepeatExpansion_TA";
COLUMN_KEYS[28] = "RepeatExpansion_TC";
COLUMN_KEYS[29] = "RepeatExpansion_TG";
COLUMN_KEYS[30] = "RepeatExpansion_1";
COLUMN_KEYS[31] = "RepeatExpansion_2";
COLUMN_KEYS[32] = "RepeatExpansion_3";
COLUMN_KEYS[33] = "RepeatExpansion_4";
COLUMN_KEYS[34] = "RepeatExpansion_5";
COLUMN_KEYS[35] = "RepeatExpansion_6";
COLUMN_KEYS[36] = "RepeatExpansion_7";
COLUMN_KEYS[37] = "RepeatExpansion_8";
COLUMN_KEYS[38] = "RepeatExpansion_9";
COLUMN_KEYS[39] = "RepeatExpansion_10orMore";
COLUMN_KEYS[40] = "Other";
COLUMN_KEYS[30] = "EventLength_1";
COLUMN_KEYS[31] = "EventLength_2";
COLUMN_KEYS[32] = "EventLength_3";
COLUMN_KEYS[33] = "EventLength_4";
COLUMN_KEYS[34] = "EventLength_5";
COLUMN_KEYS[35] = "EventLength_6";
COLUMN_KEYS[36] = "EventLength_7";
COLUMN_KEYS[37] = "EventLength_8";
COLUMN_KEYS[38] = "EventLength_9";
COLUMN_KEYS[39] = "EventLength_10orMore";
COLUMN_KEYS[40] = "NumRepetitions_1";
COLUMN_KEYS[41] = "NumRepetitions_2";
COLUMN_KEYS[42] = "NumRepetitions_3";
COLUMN_KEYS[43] = "NumRepetitions_4";
COLUMN_KEYS[44] = "NumRepetitions_5";
COLUMN_KEYS[45] = "NumRepetitions_6";
COLUMN_KEYS[46] = "NumRepetitions_7";
COLUMN_KEYS[47] = "NumRepetitions_8";
COLUMN_KEYS[48] = "NumRepetitions_9";
COLUMN_KEYS[49] = "NumRepetitions_10orMore";
COLUMN_KEYS[50] = "Other";
}
@ -75,7 +85,9 @@ public class IndelUtils {
private static final int STOP_IND_FOR_REPEAT_EXPANSION_2 = 29;
private static final int START_IND_FOR_REPEAT_EXPANSION_COUNTS = 30;
private static final int STOP_IND_FOR_REPEAT_EXPANSION_COUNTS = 39;
private static final int IND_FOR_OTHER_EVENT = 40;
private static final int START_IND_FOR_NUM_REPETITION_COUNTS = 40;
private static final int STOP_IND_FOR_NUM_REPETITION_COUNTS = 49;
private static final int IND_FOR_OTHER_EVENT = 50;
private static final int START_IND_NOVEL_PER_BASE = 0;
private static final int STOP_IND_NOVEL_PER_BASE = 3;
@ -182,11 +194,18 @@ public class IndelUtils {
}
}
else {
int ind = START_IND_FOR_REPEAT_EXPANSION_COUNTS + (numRepetitions-1);
if (ind > STOP_IND_FOR_REPEAT_EXPANSION_COUNTS)
ind = STOP_IND_FOR_REPEAT_EXPANSION_COUNTS;
// log number of repetition counts
int ind = START_IND_FOR_NUM_REPETITION_COUNTS + (numRepetitions-1);
if (ind > STOP_IND_FOR_NUM_REPETITION_COUNTS)
ind = STOP_IND_FOR_NUM_REPETITION_COUNTS;
inds.add(ind);
ind = START_IND_FOR_REPEAT_EXPANSION_COUNTS + (eventLength - 1);
if (ind > STOP_IND_FOR_REPEAT_EXPANSION_COUNTS)
ind = STOP_IND_FOR_REPEAT_EXPANSION_COUNTS;
inds.add(ind);
// log event length
if (eventLength<=2) {
// for single or dinucleotide indels, we further log the base in which they occurred
String keyStr = "RepeatExpansion_" + indelAlleleString;
@ -199,6 +218,7 @@ public class IndelUtils {
inds.add(k);
}
}
return inds;