I am using samtools v1.6 to get some stats on my bam file. Here, I merged my two paired end reads and ran bwa twice, once on merged reads and once on unmerged reads and then merged the two .bam files using samtools merge. I then used both samtools stats and samtools flagstat to get some stats but interestingly, I get different results. Can you help me understand why?
samtools flagstat Sample_sorted.bam 60970 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 8465 + 0 supplementary 0 + 0 duplicates 45003 + 0 mapped (73.81% : N/A) 27856 + 0 paired in sequencing 13046 + 0 read1 14810 + 0 read2 0 + 0 properly paired (0.00% : N/A) 22138 + 0 with itself and mate mapped 1051 + 0 singletons (3.77% : N/A) 19562 + 0 with mate mapped to a different chr 4 + 0 with mate mapped to a different chr (mapQ>=5) samtools stats Sample_sorted.bam |grep ^SN | cut -f 2- raw total sequences: 52505 filtered sequences: 0 sequences: 52505 is sorted: 1 1st fragments: 37695 last fragments: 14810 reads mapped: 36538 reads mapped and paired: 22138 # paired-end technology bit set + both mates mapped reads unmapped: 15967 reads properly paired: 0 # proper-pair bit set reads paired: 27856 # paired-end technology bit set reads duplicated: 0 # PCR or optical duplicate bit set reads MQ0: 36523 # mapped and MQ=0 reads QC failed: 0 non-primary alignments: 0 total length: 7949149 # ignores clipping bases mapped: 6010513 # ignores clipping bases mapped (cigar): 5909812 # more accurate bases trimmed: 0 bases duplicated: 0 mismatches: 484745 # from NM fields error rate: 8.202376e-02 # mismatches / bases mapped (cigar) average length: 151 maximum length: 293 average quality: 35.5 insert size average: 267.3 insert size standard deviation: 229.1 inward oriented pairs: 1005 outward oriented pairs: 134 pairs with other orientation: 3 pairs on different chromosomes: 9781
I also did a simple count on my bam file and it aligns with samtools flagstat results but not stats results.
samtools view Sample_sorted.bam | wc -l 60970