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Update documentation in the new help system 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2380 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-12-16 21:33:12 +00:00
parent ee47eb4367
commit 36875fca89
4 changed files with 16 additions and 15 deletions
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13
java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java
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@ -16,12 +16,10 @@ import java.util.List;
import java.util.Set;
/**
* Created by IntelliJ IDEA.
* User: andrewk
* Date: Sep 1, 2009
* Time: 11:04:55 AM
* To change this template use File | Settings | File Templates.
* Implements a rudimentary algorithm for calling SNPs that are de novo in that they appear in an individual but not in
* its parents.
*/
@By(DataSource.REFERENCE)
@Requires(value={DataSource.REFERENCE, DataSource.REFERENCE_BASES, DataSource.READS},referenceMetaData={@RMD(name="child",type= VariationRod.class)})
@Allows({DataSource.READS, DataSource.REFERENCE})
@ -29,6 +27,11 @@ import java.util.Set;
//, @RMD(name="parent1",type= VariationRod.class), @RMD(name="parent2",type= VariationRod.class)})
public class DeNovoSNPWalker extends RefWalker<String, Integer>{
/**
* Implements a rudimentary algorithm for calling SNPs that are de novo in that they appear in an individual but not in
* its parents. Using BAM files corresponding to parents and child, it calls UnifiedGenotyper directly and outputs a
* confidence for positions being de novo SNPs.
* */
UnifiedGenotyper UG;
private List<Set<String>> readGroupSets;

7
java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java
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@ -20,11 +20,8 @@ import java.util.Arrays;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: andrewk
* Date: Jun 30, 2009
* Time: 12:38:17 PM
* To change this template use File | Settings | File Templates.
* Given a set of reads and truth data from a HapMap chip, this walker downsamples the reads at variant
* positions to empirically assess the rate at which variants would be confidently and correctly called given different levels of coverage.
*/
public class SnpCallRateByCoverageWalker extends LocusWalker<List<String>, String> {

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java
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@ -16,11 +16,7 @@ import java.util.ArrayList;
import java.util.Arrays;
/**
* Created by IntelliJ IDEA.
* User: andrewk
* Date: Oct 20, 2009
* Time: 5:00:53 PM
* To change this template use File | Settings | File Templates.
* Accumulates coverage across hybrid selection bait intervals to assess effect of bait adjacency and overlap on coverage
*/
@By(DataSource.REFERENCE)

5
java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java
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@ -24,6 +24,11 @@ import edu.mit.broad.picard.util.Interval;
import edu.mit.broad.picard.util.OverlapDetector;
import edu.mit.broad.picard.directed.IntervalList;
/**
* Given intervals corresponding to targets or baits in a hybrid selection experiment, this walker gives the following interval-by-interval data:
* coverage, %GC, corresponding gene name, bait quantity, number of adjacent baits, and whether the bait is boosted.
* It can be useful to manually disable the merging of intervals in the GATK when using this walker; this feature is not yet part of the GATK.
*/
@By(DataSource.REFERENCE)
public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerformanceWalker.TargetInfo> implements TreeReducible<HybSelPerformanceWalker.TargetInfo> {
@Argument(fullName="min_mapq", shortName="mmq", required=false, doc="Minimum mapping quality of reads to consider")