Bowtie1 command specification

bowtie -q -n 1 -m 1 -p 12 --phred64-quals ${dir_bt1}GRCh37.p13.genome $TMPDIR/$fastq $TMPDIR/$mapf > $TMPDIR/$logf

-q
Input file is fastq format. Also the default setting

-p
Number of processors to use

-n
Maximum number of mismatches permitted. This may be 0, 1, 2 or 3. Default is 2.

-m
Suppress all alignments if more than <int> reportable alignments exist for it.

-S
Print alignments in the SAM format