Merge pull request #894 from broadinstitute/gg_ami_docs_license
Edited ASEReadCounter documentation
This commit is contained in:
Geraldine Van der Auwera
commit
87b3dddb39
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@ -44,25 +44,38 @@ import java.io.PrintStream;
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import java.util.List;
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/**
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* Calculated allele counts in specific loci, to allow allele specific expression analysis.
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* Calculate allele counts for allele-specific expression analysis
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*
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* <p>
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* Calculated allele counts in specific loci after filtering based on mapping quality, base quality, depth of coverage, overlapping paired reads and deletion on the position.
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* All thresholds and option can be set as command line arguments.
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* The output of this tool is a tab delimited txt file, compatible with Mamba, a downstream tool (http://www.well.ox.ac.uk/~rivas/mamba/).
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* A user can use -drf DuplicateRead to allow the tool to count also duplicated reads (a useful option for RNAseq data tools)
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* This tool calculates allele counts at a set of given loci after applying filters that are tuned for enabling
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* allele-specific expression (ASE) analysis. The filters operate on mapping quality, base quality, depth of coverage,
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* overlapping paired reads and deletions overlapping the position. All thresholds and options are controlled by
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* command-line arguments.
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* </p>
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*
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* <h4>Notes</h4>
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* <ul>
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* <li>Like most GATK tools, this tools filters out duplicate reads by default. However, some ASE methods
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* recommend including duplicate reads in the analysis, so the DuplicateReads filter can be disabled using the
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* `-drf DuplicateReads` flag in the command-line.</li>
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* </ul>
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* <h4>Caveats</h4>
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* <ul>
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* <li>This tool will only process biallelic sites. If your callset contains multiallelic sites, they will be ignored.
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* Optionally, you can subset your callset to just biallelic variants using e.g.
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* <a href="org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php">SelectVariants</a>
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* with the option `-restrictAllelesTo BIALLELIC`.</li>
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* </ul>
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* <h3>Input</h3>
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* <p>
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* BAM files (with proper headers) to be analyzed for ASE * </p>
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* <p>
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* a VCF file with specific sites to process
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* </p>
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* <ul>
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* <li>BAM files (with proper headers) to be analyzed for ASE</li>
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* <li>A VCF file with specific sites to process.</li>
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* </p></p>
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* <h3>Output</h3>
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* <p>
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* Table (tab delimited file) with the specific allele counts
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* A table of allele counts at the given sites. By default, it is formatted as a tab-delimited text file
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* that is readable by R and compatible with <a href="http://www.well.ox.ac.uk/~rivas/mamba/">Mamba</a>,
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* a downstream tool developed for allele-specific expression analysis.
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* </p>
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*
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* <h3>Examples</h3>
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@ -72,11 +85,11 @@ import java.util.List;
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* -T ASEReadCounter \
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* -o file_name \
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* -I input.bam \
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* -sites sites.vcf
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* -U ALLOW_N_CIGAR_READS
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* -sites sites.vcf \
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* -U ALLOW_N_CIGAR_READS \
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* [-minDepth 10] \
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* [--minMappingQuality 10] \
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* [--minBaseQuality 2]
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* [--minBaseQuality 2] \
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* [-drf DuplicateRead]
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* </pre>
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*/
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@ -91,38 +104,40 @@ public class ASEReadCounter extends LocusWalker<String, Integer> {
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public RodBinding<VariantContext> sites;
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/**
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* Loci with total depth lower then this threshold will be skipped. This is set to -1 by default to disable the evaluation and ignore this threshold.
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* If this argument is enabled, loci with total depth lower than this threshold after all filters have been applied
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* will be skipped. This is set to -1 by default to disable the evaluation and ignore this threshold.
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*/
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@Argument(fullName = "minDepthOfNonFilteredBase", shortName = "minDepth", doc = "Minimum number of filtered-pass bases that we need to see for reporting this site", required = false, minValue = 0, maxValue = Integer.MAX_VALUE)
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@Argument(fullName = "minDepthOfNonFilteredBase", shortName = "minDepth", doc = "Minimum number of bases that pass filters", required = false, minValue = 0, maxValue = Integer.MAX_VALUE)
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public int minDepthOfNonFilteredBases = -1;
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/**
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* Reads with mapping quality values lower than this threshold will be skipped. This is set to -1 by default to disable the evaluation and ignore this threshold.
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* If this argument is enabled, reads with mapping quality values lower than this threshold will not be counted.
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* This is set to -1 by default to disable the evaluation and ignore this threshold.
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*/
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@Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth", required = false, minValue = 0, maxValue = Integer.MAX_VALUE)
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@Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum read mapping quality", required = false, minValue = 0, maxValue = Integer.MAX_VALUE)
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public int minMappingQuality = 0;
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/**
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* Bases with quality scores lower than this threshold will be skipped. This is set to -1 by default to disable the evaluation and ignore this threshold.
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* If this argument is enabled, bases with quality scores lower than this threshold will not be counted.
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* This is set to -1 by default to disable the evaluation and ignore this threshold.
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*/
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@Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth", required = false, minValue = 0, maxValue = Byte.MAX_VALUE)
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@Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum base quality", required = false, minValue = 0, maxValue = Byte.MAX_VALUE)
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public byte minBaseQuality = 0;
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/**
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* There are few option to deal with an overlapping read pair.
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* COUNT_READS - Count all reads independently (even if from the same fragment).
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* COUNT_FRAGMENTS - Count all fragments (even if the reads that compose the fragment are not consistent at that base).
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* COUNT_FRAGMENTS_REQUIRE_SAME_BASEQUIRE_SAME_BASE - Count all fragments (but only if the reads that compose the fragment are consistent at that base).
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* defaults to COUNT_FRAGMENTS_REQUIRE_SAME_BASEQUIRE_SAME_BASE
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* These options modify how the tool deals with overlapping read pairs.
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* COUNT_READS - Count all reads independently, even if they are from the same fragment.
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* COUNT_FRAGMENTS - Count all fragments, even if the reads that compose the fragment are not consistent at that base.
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* COUNT_FRAGMENTS_REQUIRE_SAME_BASE - Count all fragments, but only if the reads that compose the fragment are consistent at that base (default).
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*/
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@Argument(fullName = "countOverlapReadsType", shortName = "overlap", doc = "How should overlapping reads from the same fragment be handled. Current options: COUNT_READS, COUNT_FRAGMENTS and COUNT_FRAGMENTS_REQUIRE_SAME_BASEQUIRE_SAME_BASE (default)", required = false)
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@Argument(fullName = "countOverlapReadsType", shortName = "overlap", doc = "Handling of overlapping reads from the same fragment", required = false)
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public CoverageUtils.CountPileupType countType = CoverageUtils.CountPileupType.COUNT_FRAGMENTS_REQUIRE_SAME_BASE;
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/**
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* Output file format (e.g. csv, table, rtable); defaults to r-readable table.
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* Available options are csv, table, rtable. By default, the format is an r-readable table.
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*/
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@Argument(fullName = "outputFormat", doc = "The format of the output file, can be csv, table, rtable", required = false)
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public String outputFormat = "rtable";
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@Argument(fullName = "outputFormat", doc = "Format of the output file, can be CSV, TABLE, RTABLE", required = false)
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public OUTPUT_FORMAT outputFormat = OUTPUT_FORMAT.RTABLE;
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/**
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* Consider a spanning deletion as contributing to coverage. Also enables deletion counts in per-base output.
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@ -135,9 +150,14 @@ public class ASEReadCounter extends LocusWalker<String, Integer> {
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@Argument(fullName = "ignoreDeletionSites", doc = "Ignore sites consisting only of deletions", required = false)
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public boolean ignoreDeletionSites = false;
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final String[] OUTPUT_FORMATS = {"table","rtable","csv"};
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public String separator = "\t";
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public enum OUTPUT_FORMAT{
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TABLE,
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RTABLE,
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CSV
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}
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////////////////////////////////////////////////////////////////////////////////////
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// STANDARD WALKER METHODS
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////////////////////////////////////////////////////////////////////////////////////
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@ -148,15 +168,15 @@ public class ASEReadCounter extends LocusWalker<String, Integer> {
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// Check the output format
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boolean goodOutputFormat = false;
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for ( final String f : OUTPUT_FORMATS ) {
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for ( final OUTPUT_FORMAT f : OUTPUT_FORMAT.values()) {
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goodOutputFormat = goodOutputFormat || f.equals(outputFormat);
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}
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if ( ! goodOutputFormat ) {
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throw new IllegalArgumentException("Improper output format. Can be one of table,rtable,csv. Was "+outputFormat);
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throw new IllegalArgumentException("Improper output format. Can be one of TABLE, RTABLE, CSV. Was "+outputFormat);
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}
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if ( outputFormat.equals("csv") ) {
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if ( outputFormat.equals(OUTPUT_FORMAT.CSV) ) {
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separator = ",";
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}
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final String header = "contig"+separator+"position"+separator+"variantID"+separator+"refAllele"+separator+"altAllele"+separator+"refCount"+separator+"altCount"+separator+"totalCount"+separator+"lowMAPQDepth"+separator+"lowBaseQDepth"+separator+"rawDepth"+separator+"otherBases"+separator+"improperPairs";
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@ -176,13 +196,13 @@ public class ASEReadCounter extends LocusWalker<String, Integer> {
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final List<VariantContext> VCs = tracker.getValues(sites, context.getLocation());
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if(VCs != null && VCs.size() > 1)
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throw new UserException("more then one variant context in position: "+contig+":"+position);
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throw new UserException("More then one variant context at position: "+contig+":"+position);
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if(VCs == null || VCs.size() == 0)
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return null;
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final VariantContext vc = VCs.get(0);
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if(!vc.isBiallelic()) {
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logger.warn("ignore site: cannot run ASE on non-biallelic sites: " + vc.toString());
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logger.warn("Ignoring site: cannot run ASE on non-biallelic sites: " + vc.toString());
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return null;
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}
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