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  • m_elena_bioinfo
    Member
    • Oct 2009
    • 99

    depth of coverage outputs gatk

    Hi to everybody,
    I run
    > java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R hg19.fasta -I sample.bam.sorted.bam -L chr22 --minMappingQuality 20 -o coverage.txt

    and the script returns me different outputs:

    1.sample_cumulative_coverage_counts
    2. sample_cumulative_coverage_proportions
    3. sample_interval_statistics
    4. sample_interval_summary
    5. sample_statistics
    6. sample_summary

    Anyone could explain me these outputs?

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