Examples of picard.illumina.CollectIlluminaSummaryMetrics

picard.illumina.CollectIlluminaSummaryMetrics

Program to collect Coverage Summary Metrics of SAM files for data sequenced by Illumina products. It uses our best approximation of the filters that Illumina uses which means:

1. Examine PF reads only 2. Examine reads that are not marked as duplicate only 3. Examine mapped reads only (it is unclear if Illumina does this or not, but without this we cannot do the next point) 4. Only count bases that are present in two of mated reads, once. (For this we need TLEN from the sam record, which required that reads are mapped) Program assumes that all reads in the SAM file are of equal length. @author farjoun@broadinstitute.org

        if(!intervalFile.equals("")) argList.add("TARGET_REGION="+intervalFile);


        final String[] args = new String[argList.size()];
        argList.toArray(args);


        Assert.assertEquals(new CollectIlluminaSummaryMetrics().instanceMain(args), 0);


        final MetricsFile<IlluminaSummaryMetrics, Integer> retVal = new MetricsFile<IlluminaSummaryMetrics, Integer>();
        retVal.read(new FileReader(outputFile));
        return retVal;
    }

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