diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index fa3991694..426c10604 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -65,10 +65,51 @@ import java.util.*; /** * Performs local realignment of reads based on misalignments due to the presence of indels. - * Unlike most mappers, this walker uses the full alignment context to determine whether an - * appropriate alternate reference (i.e. indel) exists and updates SAMRecords accordingly. + * + *

+ * The local realignment tool is designed to consume one or more BAM files and to locally realign reads such that the number of mismatching bases + * is minimized across all the reads. In general, a large percent of regions requiring local realignment are due to the presence of an insertion + * or deletion (indels) in the individualÕs genome with respect to the reference genome. Such alignment artifacts result in many bases mismatching + * the reference near the misalignment, which are easily mistaken as SNPs. Moreover, since read mapping algorithms operate on each read independently, + * it is impossible to place reads on the reference genome such at mismatches are minimized across all reads. Consequently, even when some reads are + * correctly mapped with indels, reads covering the indel near just the start or end of the read are often incorrectly mapped with respect the true indel, + * also requiring realignment. Local realignment serves to transform regions with misalignments due to indels into clean reads containing a consensus + * indel suitable for standard variant discovery approaches. Unlike most mappers, this walker uses the full alignment context to determine whether an + * appropriate alternate reference (i.e. indel) exists. Following local realignment, the GATK tool Unified Genotyper can be used to sensitively and + * specifically identify indels. + *

+ *

    There are 2 steps to the realignment process: + *
  1. Determining (small) suspicious intervals which are likely in need of realignment (see the RealignerTargetCreator tool)
    2. + *
  2. Running the realigner over those intervals (IndelRealigner)
    3. + *
+ *

+ * An important note: because reads produced from the 454 technology inherently contain false indels, the realigner will not currently work with them + * (or with reads from similar technologies). + * + *

Input

+ *

+ * One or more aligned BAM files and optionally one or more lists of known indels. + *

+ * + *

Output

+ *

+ * A realigned version of your input BAM file(s). + *

+ * + *

Examples

+ * 
+ * java -Xmx4g -jar GenomeAnalysisTK.jar \
+ *   -I  \
+ *   -R  \
+ *   -T IndelRealigner \
+ *   -targetIntervals  \
+ *   -o  \
+ *   [--known /path/to/indels.vcf] \
+ *   [-compress 0]    (this argument recommended to speed up the process *if* this is only a temporary file; otherwise, use the default value)
+ *
+ * + * @author ebanks */ -//Reference(window=@Window(start=-30,stop=30)) @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT) public class IndelRealigner extends ReadWalker { @@ -77,88 +118,136 @@ public class IndelRealigner extends ReadWalker { public static final String PROGRAM_RECORD_NAME = "GATK IndelRealigner"; public enum ConsensusDeterminationModel { + /** + * Uses only indels from a provided ROD of known indels. + */ KNOWNS_ONLY, + /** + * Additionally uses indels already present in the original alignments of the reads. + */ USE_READS, + /** + * Additionally uses 'Smith-Waterman' to generate alternate consenses. + */ USE_SW } - @Input(fullName="known", shortName = "known", doc="Input VCF file with known indels", required=false) + /** + * Any number of VCF files representing known indels to be used for constructing alternate consenses. + * Could be e.g. dbSNP and/or official 1000 Genomes indel calls. Non-indel variants in these files will be ignored. + */ + @Input(fullName="known", shortName = "known", doc="Input VCF file(s) with known indels", required=false) public List> known = Collections.emptyList(); + /** + * The interval list output from the RealignerTargetCreator tool using the same bam(s), reference, and known indel file(s). + */ @Input(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true) protected String intervalsFile = null; + /** + * This term is equivalent to "significance" - i.e. is the improvement significant enough to merit realignment? Note that this number + * should be adjusted based on your particular data set. For low coverage and/or when looking for indels with low allele frequency, + * this number should be smaller. + */ @Argument(fullName="LODThresholdForCleaning", shortName="LOD", doc="LOD threshold above which the cleaner will clean", required=false) protected double LOD_THRESHOLD = 5.0; - @Argument(fullName="entropyThreshold", shortName="entropy", doc="percentage of mismatches at a locus to be considered having high entropy", required=false) - protected double MISMATCH_THRESHOLD = 0.15; - + /** + * The realigned bam file. + */ @Output(required=false, doc="Output bam") protected StingSAMFileWriter writer = null; protected ConstrainedMateFixingManager manager = null; protected SAMFileWriter writerToUse = null; - @Argument(fullName = "consensusDeterminationModel", shortName = "model", doc = "How should we determine the possible alternate consenses? -- in the order of least permissive to most permissive there is KNOWNS_ONLY (use only indels from known indels provided in RODs), USE_READS (additionally use indels already present in the original alignments of the reads), and USE_SW (additionally use 'Smith-Waterman' to generate alternate consenses). The default is USE_READS", required = false) + /** + * We recommend that users run with USE_READS when trying to realign high quality longer read data mapped with a gapped aligner; + * Smith-Waterman is really only necessary when using an ungapped aligner (e.g. MAQ in the case of single-end read data). + */ + @Argument(fullName = "consensusDeterminationModel", shortName = "model", doc = "Determines how to compute the possible alternate consenses", required = false) public ConsensusDeterminationModel consensusModel = ConsensusDeterminationModel.USE_READS; // ADVANCED OPTIONS FOLLOW - @Argument(fullName="maxReadsInMemory", shortName="maxInMemory", doc="max reads allowed to be kept in memory at a time by the SAMFileWriter. "+ - "Keep it low to minimize memory consumption (but the tool may skip realignment on regions with too much coverage. If it is too low, it may generate errors during realignment); keep it high to maximize realignment (but make sure to give Java enough memory).", required=false) + /** + * For expert users only! This is similar to the argument in the RealignerTargetCreator walker. The point here is that the realigner + * will only proceed with the realignment (even above the given threshold) if it minimizes entropy among the reads (and doesn't simply + * push the mismatch column to another position). This parameter is just a heuristic and should be adjusted based on your particular data set. + */ + @Argument(fullName="entropyThreshold", shortName="entropy", doc="percentage of mismatches at a locus to be considered having high entropy", required=false) + protected double MISMATCH_THRESHOLD = 0.15; + + /** + * For expert users only! To minimize memory consumption you can lower this number (but then the tool may skip realignment on regions with too much coverage; + * and if the number is too low, it may generate errors during realignment). Just make sure to give Java enough memory! 4Gb should be enough with the default value. + */ + @Argument(fullName="maxReadsInMemory", shortName="maxInMemory", doc="max reads allowed to be kept in memory at a time by the SAMFileWriter", required=false) protected int MAX_RECORDS_IN_MEMORY = 150000; + /** + * For expert users only! + */ @Argument(fullName="maxIsizeForMovement", shortName="maxIsize", doc="maximum insert size of read pairs that we attempt to realign", required=false) protected int MAX_ISIZE_FOR_MOVEMENT = 3000; + /** + * For expert users only! + */ @Argument(fullName="maxPositionalMoveAllowed", shortName="maxPosMove", doc="maximum positional move in basepairs that a read can be adjusted during realignment", required=false) protected int MAX_POS_MOVE_ALLOWED = 200; + /** + * For expert users only! If you need to find the optimal solution regardless of running time, use a higher number. + */ @Argument(fullName="maxConsensuses", shortName="maxConsensuses", doc="max alternate consensuses to try (necessary to improve performance in deep coverage)", required=false) protected int MAX_CONSENSUSES = 30; + /** + * For expert users only! If you need to find the optimal solution regardless of running time, use a higher number. + */ @Argument(fullName="maxReadsForConsensuses", shortName="greedy", doc="max reads used for finding the alternate consensuses (necessary to improve performance in deep coverage)", required=false) protected int MAX_READS_FOR_CONSENSUSES = 120; - @Argument(fullName="maxReadsForRealignment", shortName="maxReads", doc="max reads allowed at an interval for realignment; "+ - "if this value is exceeded, realignment is not attempted and the reads are passed to the output file(s) as-is", required=false) + /** + * For expert users only! If this value is exceeded at a given interval, realignment is not attempted and the reads are passed to the output file(s) as-is. + * If you need to allow more reads (e.g. with very deep coverage) regardless of memory, use a higher number. + */ + @Argument(fullName="maxReadsForRealignment", shortName="maxReads", doc="max reads allowed at an interval for realignment", required=false) protected int MAX_READS = 20000; - @Argument(fullName="noPGTag", shortName="noPG", required=false, - doc="Don't output the usual PG tag in the realigned bam file header. FOR DEBUGGING PURPOSES ONLY. "+ - "This option is required in order to pass integration tests.") - protected boolean NO_PG_TAG = false; - - @Argument(fullName="noOriginalAlignmentTags", shortName="noTags", required=false, - doc="Don't output the original cigar or alignment start tags for each realigned read in the output bam.") + @Argument(fullName="noOriginalAlignmentTags", shortName="noTags", required=false, doc="Don't output the original cigar or alignment start tags for each realigned read in the output bam") protected boolean NO_ORIGINAL_ALIGNMENT_TAGS = false; - @Argument(fullName="targetIntervalsAreNotSorted", shortName="targetNotSorted", required=false, - doc="This tool assumes that the target interval list is sorted; if the list turns out to be unsorted, "+ - "it will throw an exception. Use this argument when your interval list is not sorted to instruct "+"" + - "the Realigner to first sort it in memory.") + /** + * For expert users only! This tool assumes that the target interval list is sorted; if the list turns out to be unsorted, it will throw an exception. + * Use this argument when your interval list is not sorted to instruct the Realigner to first sort it in memory. + */ + @Argument(fullName="targetIntervalsAreNotSorted", shortName="targetNotSorted", required=false, doc="The target intervals are not sorted") protected boolean TARGET_NOT_SORTED = false; - //NWay output: testing, not ready for the prime time, hence hidden: - - @Hidden - @Argument(fullName="nWayOut", shortName="nWayOut", required=false, - doc="Generate one output file for each input (-I) bam file. Reads from all input files "+ - "will be realigned together, but then each read will be saved in the output file corresponding to "+ - "the input file the read came from. There are two ways to generate output bam file names: 1) if the "+ - "value of this argument is a general string (e.g. '.cleaned.bam'), then "+ - "extensions (\".bam\" or \".sam\") will be stripped from the input file names and the provided string value "+ - "will be pasted on instead; 2) if the value ends with a '.map' (e.g. input_output.map), then " + - "the two-column tab-separated file with the specified name must exist and list unique output file name (2nd column)" + - "for each input file name (1st column).") + /** + * Reads from all input files will be realigned together, but then each read will be saved in the output file corresponding to the input file that + * the read came from. There are two ways to generate output bam file names: 1) if the value of this argument is a general string (e.g. '.cleaned.bam'), + * then extensions (".bam" or ".sam") will be stripped from the input file names and the provided string value will be pasted on instead; 2) if the + * value ends with a '.map' (e.g. input_output.map), then the two-column tab-separated file with the specified name must exist and list unique output + * file name (2nd column) for each input file name (1st column). + */ + @Argument(fullName="nWayOut", shortName="nWayOut", required=false, doc="Generate one output file for each input (-I) bam file") protected String N_WAY_OUT = null; + + + // DEBUGGING OPTIONS FOLLOW + @Hidden @Argument(fullName="check_early",shortName="check_early",required=false,doc="Do early check of reads against existing consensuses") protected boolean CHECKEARLY = false; - - // DEBUGGING OPTIONS FOLLOW + @Hidden + @Argument(fullName="noPGTag", shortName="noPG", required=false, + doc="Don't output the usual PG tag in the realigned bam file header. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.") + protected boolean NO_PG_TAG = false; @Hidden @Output(fullName="indelsFileForDebugging", shortName="indels", required=false, doc="Output file (text) for the indels found; FOR DEBUGGING PURPOSES ONLY")