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

Picard CollectWGSMetrics vs QualiMap vs samtools stats


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    Gökalp Çelik

    Hi Damian Fermin

    These tools all use different thresholds to accept reads for calculation. 

    Picard CollectWgsMetrics uses the below parameters as default and therefore may end up reporting a lower coverage. You may set both parameters to 0 to compare your results with others. 

                                  Minimum base quality for a base to contribute coverage. N bases will be treated as having
                                  a base quality of negative infinity and will therefore be excluded from coverage
                                  regardless of the value of this parameter.  Default value: 20. 

                                  Minimum mapping quality for a read to contribute coverage.  Default value: 20.

    There are also other parameters present such as COVERAGE_CAP and LOCUS_ACCUMULATION_CAP both of which may affect your output. 

    I hope this helps. 

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