Defination of PF_ALIGNED_BASES and PF_INDEL_RATE
Hi,
I am using Picard (2.9.0) CollectAlignmentSummaryMetrics. May I ask how PF_ALIGNED_BASES is counted? Does it include both match and mismatched bases and exclude all indels, gaps and soft/hard clips? Does PF_MISMATCH_RATE * PF_ALIGNED_BASES equal the total number of mismatched bases?
Also, could I get the number of indel events by calculating PF_INDEL_RATE * PF_ALIGNED_BASES / 100 based on the documentation of CollectAlignmentSummaryMetrics? Thank you!
Thank you!
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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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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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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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