Re: [Samtools-help] Filter reads with multiple flags - samtools view

[Peter <pe...@ma...>]

On Mon, Feb 28, 2011 at 7:50 AM, Praveen Raj <pra...@gm...> wrote:
> Just wanted to know how to provide multiple flags at same time to filter out
> reads from BAM when using "samtools view" command? For Eg: If I want to
> apply(extract) reads based on two flags (say "-f 0x02" and "-f 0x08") from
> BAM, what should be the appropriate way to do this? It seems repeating "-f"
> with each flag in command-line doesnot help.
> Any advice on this would be great help.
> Praveen Raj

I've never tried, but in that case try combining the desired flags, 0x02 plus/or
0x08 is 0x0A (in binary, 2+8=10), so I'd expect -f 0x0A will do what you want.

Peter