From 36875fca89f1612b7cc7dd16cdda99f8876af567 Mon Sep 17 00:00:00 2001 From: andrewk Date: Wed, 16 Dec 2009 21:33:12 +0000 Subject: [PATCH] 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 --- .../playground/gatk/walkers/DeNovoSNPWalker.java | 13 ++++++++----- .../gatk/walkers/SnpCallRateByCoverageWalker.java | 7 ++----- .../hybridselection/CoverageAcrossBaitsWalker.java | 6 +----- .../hybridselection/HybSelPerformanceWalker.java | 5 +++++ 4 files changed, 16 insertions(+), 15 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java index 9fbe2c3e3..49f0c3a53 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java @@ -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{ +/** + * 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> readGroupSets; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java index 52989b833..fdda3df4a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java @@ -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, String> { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java index d58632400..39a77588b 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java @@ -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) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java index 615deec16..fe6209f88 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java @@ -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 implements TreeReducible { @Argument(fullName="min_mapq", shortName="mmq", required=false, doc="Minimum mapping quality of reads to consider")