Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

CollectHsMetrics (Picard) Follow

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    Eva (Evander)

    Dear GATK,

    Could I suggest a more concise section on what is filtered in the ouput of HSmetrics per target metrics? Because I was thoroughly confused about why I was not getting any coverage on some regions in the per target metrics file. Turns our you do not show coverage/reads (I guess) below < 20 MAPQ. I had to find out through the documentation of another tool (CollectWgsMetrics).

    This was in the CollectHsMetrics:


    The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.

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