Get random alignments from SAM file

[komalsrathi]

Hi all,

I have a .sam file and I want to extract random alignments from it.

I googled a bit and there are quite a few tools that have commands to "downsample a sam file" like Picard and GATK. I couldn't really find if these tools would allow me to extract a certain percentage or certain number of alignments from the SAM file.

I also got an alternative which would allow me to do that from http://www.biostars.org/p/44527/

But I would like to do the same thing using Picard or GATK. Any suggestions?

[lh3]

That biostar thread seems quite clear to me. It provides solutions with either samtools or picard.

[komalsrathi]

I know, I just can't find a delete option for this post!