samstat output is different than bowtie2 stats

[bounlu]

The output stats from bowtie2 and samstat on the same bam file are different:

bowtie2:

18657869 reads; of these:
  18657869 (100.00%) were unpaired; of these:
    1995321 (10.69%) aligned 0 times
    12773937 (68.46%) aligned exactly 1 time
    3888611 (20.84%) aligned >1 times
89.31% overall alignment rate

samstat:

any explanation?

[TimoLassmann]

Samstat works only on SAM/BAM lines that represent primary alignments and excludes all reads that fail platform/vendor quality checks. I suspect that this is where the discrepancies come from.

[bounlu]

I see, you are using the flag -F 768. Thanks for the info.