Improved gatkdocs for InbreedingCoefficient, ReduceReads, ErrorRatePerCycle
Clarified caveat for InbreedingCoefficient Cleaned up docstrings for ReduceReads Brushed up doc for ErrorRatePerCycle
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Geraldine Van der Auwera
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@ -70,8 +70,8 @@ import java.util.*;
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*
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* A continuous generalization of the Hardy-Weinberg test for disequilibrium that works
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* well with limited coverage per sample. See the 1000 Genomes Phase I release for
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* more information. Note that the Inbreeding Coefficient will not be calculated for files
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* with fewer than a minimum (generally 10) number of samples.
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* more information. Note that the Inbreeding Coefficient can only be calculated for
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* cohorts containing at least 10 founder samples.
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*/
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public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
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@ -84,10 +84,10 @@ import java.util.List;
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* Reduces the BAM file using read based compression that keeps only essential information for variant calling
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*
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* <p>
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* This walker will generated reduced versions of the BAM files that still follow the BAM spec
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* and contain all the information necessary for the GSA variant calling pipeline. Some options
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* allow you to tune in how much compression you want to achieve. The default values have been
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* shown to reduce a typical whole exome BAM file 100x. The higher the coverage, the bigger the
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* This tool will generate reduced versions of the BAM files that still follow the BAM specification
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* and contain all the information necessary to call variants according to the GATK Best Practices recommendations.
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* Some options allow you to tune how much compression you want to achieve. The default values have been
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* shown to reduce a typical whole exome BAM file by 100x. The higher the coverage, the bigger the
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* savings in file size and performance of the downstream tools.
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*
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* <h3>Input</h3>
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@ -121,25 +121,25 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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private SAMFileWriter writerToUse = null;
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/**
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* The number of bases to keep around mismatches (potential variation)
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*
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*/
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@Argument(fullName = "context_size", shortName = "cs", doc = "", required = false)
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@Argument(fullName = "context_size", shortName = "cs", doc = "The number of bases to keep around mismatches (potential variation)", required = false)
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public int contextSize = 10;
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/**
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* The minimum mapping quality to be considered for the consensus synthetic read. Reads that have
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* Reads that have
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* mapping quality below this threshold will not be counted towards consensus, but are still counted
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* towards variable regions.
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*/
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@Argument(fullName = "minimum_mapping_quality", shortName = "minmap", doc = "", required = false)
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@Argument(fullName = "minimum_mapping_quality", shortName = "minmap", doc = "The minimum mapping quality to be considered for the consensus synthetic read", required = false)
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public int minMappingQuality = 20;
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/**
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* The minimum base quality to be considered for the consensus synthetic read. Reads that have
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* Reads that have
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* base quality below this threshold will not be counted towards consensus, but are still counted
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* towards variable regions.
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*/
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@Argument(fullName = "minimum_base_quality_to_consider", shortName = "minqual", doc = "", required = false)
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@Argument(fullName = "minimum_base_quality_to_consider", shortName = "minqual", doc = "The minimum base quality to be considered for the consensus synthetic read", required = false)
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public byte minBaseQual = 15;
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/**
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@ -160,81 +160,77 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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public List<RodBinding<VariantContext>> known = Collections.emptyList();
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/**
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* Do not simplify read (strip away all extra information of the read -- anything other than bases, quals
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* and read group).
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* This strips away all extra information of the read -- anything other than bases, quals
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* and read group.
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*/
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@Argument(fullName = "dont_simplify_reads", shortName = "nosimplify", doc = "", required = false)
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@Argument(fullName = "dont_simplify_reads", shortName = "nosimplify", doc = "Do not simplify read", required = false)
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public boolean DONT_SIMPLIFY_READS = false;
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/**
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* Do not hard clip adaptor sequences. Note: You don't have to turn this on for reads that are not mate paired.
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* The program will behave correctly in those cases.
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* Note that it is not necessary to turn this on for reads that are not mate paired.
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* The program will behave correctly by default in those cases.
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*/
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@Argument(fullName = "dont_hardclip_adaptor_sequences", shortName = "noclip_ad", doc = "", required = false)
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@Argument(fullName = "dont_hardclip_adaptor_sequences", shortName = "noclip_ad", doc = "Do not hard clip adaptor sequences", required = false)
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public boolean DONT_CLIP_ADAPTOR_SEQUENCES = false;
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/**
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* Do not hard clip the low quality tails of the reads. This option overrides the argument of minimum tail
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* This option overrides the argument of minimum tail
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* quality.
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*/
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@Argument(fullName = "dont_hardclip_low_qual_tails", shortName = "noclip_tail", doc = "", required = false)
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@Argument(fullName = "dont_hardclip_low_qual_tails", shortName = "noclip_tail", doc = "Do not hard clip the low quality tails of the reads", required = false)
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public boolean DONT_CLIP_LOW_QUAL_TAILS = false;
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/**
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* Do not use high quality soft-clipped bases. By default, ReduceReads will hard clip away any low quality soft clipped
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* By default, ReduceReads will hard clip away any low quality soft clipped
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* base left by the aligner and use the high quality soft clipped bases in it's traversal algorithm to identify variant
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* regions. The minimum quality for soft clipped bases is the same as the minimum base quality to consider (minqual)
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*/
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@Argument(fullName = "dont_use_softclipped_bases", shortName = "no_soft", doc = "", required = false)
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@Argument(fullName = "dont_use_softclipped_bases", shortName = "no_soft", doc = "Do not use high quality soft-clipped bases", required = false)
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public boolean DONT_USE_SOFTCLIPPED_BASES = false;
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/**
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* Do not compress read names. By default, ReduceReads will compress read names to numbers and guarantee
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* By default, ReduceReads will compress read names to numbers and guarantee
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* uniqueness and reads with similar name will still have similar compressed names. Note: If you scatter/gather
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* there is no guarantee that read name uniqueness will be maintained -- in this case we recommend not compressing.
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*/
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@Argument(fullName = "dont_compress_read_names", shortName = "nocmp_names", doc = "", required = false)
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@Argument(fullName = "dont_compress_read_names", shortName = "nocmp_names", doc = "Do not compress read names", required = false)
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public boolean DONT_COMPRESS_READ_NAMES = false;
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/**
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* Optionally hard clip all incoming reads to the desired intervals. The hard clips will happen exactly at the interval
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* border.
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* The hard clips will happen exactly at the interval border.
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*/
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@Argument(fullName = "hard_clip_to_interval", shortName = "clip_int", doc = "", required = false)
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@Argument(fullName = "hard_clip_to_interval", shortName = "clip_int", doc = "Hard clip all incoming reads to the desired intervals", required = false)
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public boolean HARD_CLIP_TO_INTERVAL = false;
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/**
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* Minimum proportion of mismatches in a site to trigger a variant region. Anything below this will be
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* Anything below this will be
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* considered consensus and reduced (otherwise we will try to trigger polyploid compression). Note that
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* this value is used only regions with high coverage.
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*/
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@Advanced
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@Argument(fullName = "minimum_alt_proportion_to_trigger_variant", shortName = "minvar", doc = "", required = false)
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@Argument(fullName = "minimum_alt_proportion_to_trigger_variant", shortName = "minvar", doc = "Minimum proportion of mismatches in a site to trigger a variant region", required = false)
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public double minAltProportionToTriggerVariant = 0.05;
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/**
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* Minimum p-value from binomial distribution of mismatches in a site to trigger a variant region.
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* Any site with a value falling below this will be considered consensus and reduced (otherwise we will try to
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* trigger polyploid compression). Note that this value is used only regions with low coverage.
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*/
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@Advanced
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@Argument(fullName = "minimum_alt_pvalue_to_trigger_variant", shortName = "min_pvalue", doc = "", required = false)
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@Argument(fullName = "minimum_alt_pvalue_to_trigger_variant", shortName = "min_pvalue", doc = "Minimum p-value from binomial distribution of mismatches in a site to trigger a variant region", required = false)
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public double minAltPValueToTriggerVariant = 0.01;
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/**
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* Minimum proportion of indels in a site to trigger a variant region. Anything below this will be
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* considered consensus.
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* Anything below this will be considered consensus.
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*/
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@Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "", required = false)
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@Argument(fullName = "minimum_del_proportion_to_trigger_variant", shortName = "mindel", doc = "Minimum proportion of indels in a site to trigger a variant region", required = false)
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public double minIndelProportionToTriggerVariant = 0.05;
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/**
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* The number of reads emitted per sample in a variant region can be downsampled for better compression.
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* This level of downsampling only happens after the region has been evaluated, therefore it can
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* be combined with the engine level downsampling.
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* A value of 0 turns downsampling off.
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*/
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@Argument(fullName = "downsample_coverage", shortName = "ds", doc = "", required = false)
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@Argument(fullName = "downsample_coverage", shortName = "ds", doc = "Downsample the number of reads emitted per sample in a variant region for better compression", required = false)
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public int downsampleCoverage = 250;
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/**
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@ -243,27 +239,27 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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* To prevent users from unintentionally running the tool in a less than ideal manner, we require them
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* to explicitly enable multi-sample analysis with this argument.
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*/
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@Argument(fullName = "cancer_mode", shortName = "cancer_mode", doc = "enable multi-samples reduction for cancer analysis", required = false)
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@Argument(fullName = "cancer_mode", shortName = "cancer_mode", doc = "Enable multi-sample reduction for cancer analysis", required = false)
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public boolean ALLOW_MULTIPLE_SAMPLES = false;
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@Hidden
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@Argument(fullName = "nwayout", shortName = "nw", doc = "", required = false)
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@Argument(fullName = "nwayout", shortName = "nw", doc = "Generate separate output files per input file", required = false)
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public boolean nwayout = false;
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@Hidden
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@Argument(fullName = "", shortName = "dl", doc = "", required = false)
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@Argument(fullName = "", shortName = "dl", doc = "Debug level", required = false)
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public int debugLevel = 0;
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@Hidden
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@Argument(fullName = "", shortName = "dr", doc = "", required = false)
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@Argument(fullName = "", shortName = "dr", doc = "Debug read", required = false)
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public String debugRead = "";
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@Hidden
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@Argument(fullName = "downsample_strategy", shortName = "dm", doc = "", required = false)
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@Argument(fullName = "downsample_strategy", shortName = "dm", doc = "Downsampling strategy", required = false)
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public DownsampleStrategy downsampleStrategy = DownsampleStrategy.Normal;
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@Hidden
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@Argument(fullName = "no_pg_tag", shortName = "npt", doc ="", required = false)
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@Argument(fullName = "no_pg_tag", shortName = "npt", doc ="Discard program tags", required = false)
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public boolean NO_PG_TAG = false;
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public enum DownsampleStrategy {
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@ -297,7 +293,7 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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throw new UserException.MissingArgument("out", "the output must be provided and is optional only for certain debugging modes");
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if ( nwayout && out != null )
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throw new UserException.CommandLineException("--out and --nwayout can not be used simultaneously; please use one or the other");
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throw new UserException.CommandLineException("--out and --nwayout cannot be used simultaneously; please use one or the other");
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if ( minAltPValueToTriggerVariant < 0.0 || minAltPValueToTriggerVariant > 1.0 )
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throw new UserException.BadArgumentValue("--minimum_alt_pvalue_to_trigger_variant", "must be a value between 0 and 1 (inclusive)");
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@ -306,7 +302,7 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, Redu
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throw new UserException.BadArgumentValue("--minimum_alt_proportion_to_trigger_variant", "must be a value between 0 and 1 (inclusive)");
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if ( SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()).size() > 1 && !ALLOW_MULTIPLE_SAMPLES )
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throw new UserException.BadInput("Reduce Reads is not meant to be run for more than 1 sample at a time except for the specific case of tumor/normal pairs in cancer analysis");
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throw new UserException.BadInput("Reduce Reads is not meant to be run for more than 1 sample at a time except for the specific case of tumor/normal pairs in cancer analysis. If that is what you want to do, use the -cancer_mode flag.");
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if ( known.isEmpty() )
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knownSnpPositions = null;
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@ -44,10 +44,11 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import java.io.PrintStream;
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/**
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* Computes the read error rate per position in read (in the original 5'->3' orientation that the read had coming off the machine)
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* Compute the read error rate per position
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*
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* Emits a GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate for each read
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* group in the input BAMs FOR ONLY THE FIRST OF PAIR READS.
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* <p>This tool computes the read error rate per position in sequence reads. It does this in the original 5'->3'
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* orientation that the read had coming off the machine. It then emits a GATKReport containing readgroup, cycle,
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* mismatches, counts, qual, and error rate for each read group in the input BAMs.</p>
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*
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* <h3>Input</h3>
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* <p>
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@ -56,9 +57,9 @@ import java.io.PrintStream;
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*
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* <h3>Output</h3>
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* <p>
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* GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate.
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* A GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate.
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*
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* For example, running this tool on the NA12878 data sets:
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* For example, running this tool on the NA12878 data sets yields the following table:
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*
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* <pre>
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* ##:GATKReport.v0.2 ErrorRatePerCycle : The error rate per sequenced position in the reads
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@ -82,16 +83,20 @@ import java.io.PrintStream;
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* </pre>
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* </p>
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*
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* <h3>Examples</h3>
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* <h3>Example</h3>
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* <pre>
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* java
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* -jar GenomeAnalysisTK.jar
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* -T ErrorRatePerCycle
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* -I bundle/current/b37/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam
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* -R bundle/current/b37/human_g1k_v37.fasta
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* -o example.gatkreport.txt
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* -R human_g1k_v37.fasta
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* -I my_sequence_reads.bam
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* -o error_rates.gatkreport.txt
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* </pre>
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*
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* <h3>Caveat</h3>
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*
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* <p>Note that when it is run on paired-end sequence data, this tool only uses the first read in a pair.</p>
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*
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* @author Kiran Garimella, Mark DePristo
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*/
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
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