Exclude best-mapped reads

[seq_lover]

I have similar questions in this post:

http://seqanswers.com/forums/showthread.php?t=19537

I used the following tool to figure it out but I am not sure if all of my steps are right.

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

[manducasexta]

Thanks - I don't see a way to get what I'm looking for one pass, but perhaps I could get there with two:

samtools view -F2 theWholeEnchilada.bam >NotPerfectlyPaired.bam
samtools view -f2 -q 20 theWholeEnchilada.bam >PerfectlyPairedButLowQuality.bam

and then combine (samtools merge or picard or whatev) the output.

[swbarnes2]

Samtools view:

http://samtools.sourceforge.net/samtools.shtml

OPTIONS:

-b Output in the BAM format.
-f INT Only output alignments with all bits in INT present in the FLAG field. INT can be in hex in the format of /^0x[0-9A-F]+/ [0]
-F INT Skip alignments with bits present in INT [0]
...
-q INT Skip alignments with MAPQ smaller than INT [0]

[manducasexta]

Hi all --

I'm hoping for some insight. I've been slinging bam files on and off for a while, but trying to filter out the well-mapped reads by multiple criteria seems pretty daunting. Here's what I'm trying to do.

REMOVE all reads that meet these criteria:
1) Both ends are mapped
2) the mapping quality score is above some threshold (say 20)

I'm sure there's some clever series of steps that will get me there. They were originally aligned with BWA, fwiw wrt aligner-specific fields and interpretations.

Thanks in advance!