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samtools stats result different from samtools flagstat
1
Entering edit mode
16 months ago
snishtala03 • 10

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
samtools • 255 views
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Entering edit mode
16 months ago
snishtala03 • 10

I think I figured it out -

It looks like 60970 reads in flagstat includes the supplementary reads while stats does not count it. 52505 + 8465 = 60970

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