Adding the number of UNPAIRED_READS_EXAMINED and READ_PAIRS_EXAMINED does NOT give me the number of original file.
Here is my data: original file has 91137584, they are reliable reads by the command "samtools view -S -bq 1".
I want to remove the duplicate with picard, and hence set the "REMOVE_DUPLICATES=true". Output of metrics is:
UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE 104579 45330048 0 68012 14161407 5034139 0.312796 74939630
the duplicate marked file has 62746758, and 91137584 - 14161407*2 - 68012 give the number of reads in new bam file.
However, 104579 + 45330048*2 gave me 90764675, less than the actual number of reads in my file, 372909 reads are missing.
Could someone explain me what is going on?