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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

Defination of PF_ALIGNED_BASES and PF_INDEL_RATE

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    Gökalp Çelik

    Hi Leo

    Exactly. It only contains those bases that are aligned not those that are hard or softclipped. I am not 100% sure about whether that contains the gaps inside but I will check with the team and reply back. 

    You may check the definitions of those metrics from the link below.

    https://broadinstitute.github.io/picard/picard-metric-definitions.html#AlignmentSummaryMetrics 

    Regards. 

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    Leo

    I am trying to calculate the indel events and use PF_INDEL_RATE * PF_ALIGNED_BASES / 100 based on the documentation. But the results are not integer. 

     

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    Gökalp Çelik

    Looks totally normal. Since rate is calculated as number of insertion or deletion events per 100 bases it is possible that the rate number is also somehow rounded to be presentable. You can round those numbers to the nearest integer. 

     

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