-c
Instead of printing the alignments, only count them and print the total number. All filter options, such as -f, -F, and -q, are taken into account.

-s FLOAT
Output only a proportion of the input alignments. This subsampling acts in the same way on all of the alignment records in the same template or read pair, so it never keeps a read but not its mate.

The integer and fractional parts of the -s INT.FRAC option are used separately: the part after the decimal point sets the fraction of templates/pairs to be kept, while the integer part is used as a seed that influences which subset of reads is kept.

When subsampling data that has previously been subsampled, be sure to use a different seed value from those used previously; otherwise more reads will be retained than expected.