SAM/BAM how to retrieve all mapped reads ?

[Sylphide]

Hello,
I obtained a BAM file from BWA and would like to keep only mapped reads. Samtools view -q 1 removes reads with mapQ 0 and I would like to conserve them.
Does anyone have a solution ?
Many thanks

[nilshomer]

samtools view -F 4

See: http://picard.sourceforge.net/explain-flags.html

[prisnirath]

Hi...
I used BWA to get a sam file and used SamTools to call the variants in my reads, got huge no. of variants.
Whe I viewed my sam file using tablet app., I got hold of datasets showing variants with read depth 1.
how do I manipulate the read depth and set its min. value to be around 50 or so to call in genuine SNPs?