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[PICARD] CollectInsertSizeMetrics vs CollectAlignmentSummaryMetrics


I am getting some confusing results and not sure how to explain them. I am interested in the total number of reads from a PE library that actually mapped to our reference so we can take that into account in future library runs.

According to CollectInsertSizeMetrics, under the "READ_PAIRS" category, there were 1,967,786 for a particular sample. If I sum up the "All_Reads.fr_count" column of that same document, the sum is 1,958,005.

According to CollectAlignmentSummaryMetrics, the "TOTAL_READS" is 4,264,104, "PF_READS_ALIGNED" is 4,229,008, and "PF_HQ_ALIGNED" is 3,123,870. I am aware that these 3 categories are measuring different things, but I am trying to display that they are wildly different from the values given by CollectInsertSizeMetrics for the same sample.

I cannot find any rhyme or reason to these numbers (especially considering that with another program, FASTQC, the total number of reads for this same sample is 4,455,189).

Can anyone help with this?

Thank You!!!

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