Help with sam flags

[scami]

Hi guys
I would like to ask you a help with the sam format flag. I am using samtools to extract reads from a bam file. Briefly I need to extract all mapped reads in a certain range which is easy to achieve by using the samtools view command. However I need to extract together with the mapped reads also the eventual corresponding unmapped mates.
How can I do that?
thanks for the help!

[dpryan]

There's no built-in way to do that. If the number of reads in your region of interest is relatively small, then you can "samtools view -F foo.bam region | cut -f 1 > rnames" and then just "samtools view -f 4 foo.bam | grep -f rnames > unmapped_in_region.sam". You could also write a program to do this a bit more efficiently in python (just use a dict of the read names), or just query-sort things and then have the program look for overlaps pair at a time.

[scami]

Thanks

Thanks for the answer. Sam files I am using are very large so an ad hoc C or python script would not be the best option for me. I'll work on it anyway, thanks for the advice

[capricy]

how to extract reads 1 from a sam file

Hello, there,

I found that samtools filter function works only for bam file. What if I have a sam file, and I would like to only keep read1 (flag: 64)?

Do I need to convert this sam file back to bam?

Thanks!!

Capricy

[Brian Bushnell]

I'm pretty sure this works with sam input as well.

samtools view -Sf 64 mapped.sam

[dpryan]

I'm pretty sure this works with sam input as well.

samtools view -f 64 mapped.sam

Add a -S and that should work.

[capricy]

en. My problem seems to be the missing header

Thanks for all the replies!!