Sorted SAM output

[Vladimir Presnyak]

Hello all,

I was wondering if there is a way to produce sorted SAM files from STAR. I tried using a --outSAMtype SAM SortedByCoordinate flag, but that seems to produce an unsorted SAM.

Thanks!

[Alexander Dobin]

Hi Vladimir,

there is no way to get sorted SAM directly.

If you use --outSAMtype BAM SortedByCoordinate you will get sorted BAM.

To get the sorted SAM as your output, you can output sorted BAM to stdout, and pipe it into samtools view, i.e.

$ STAR ... --outSAMtype BAM SortedByCoordinate --outStd BAM_SortedByCoordinate | samtools view -h - > Aigned.sorted.sam

Cheers

Alex

[Vladimir Presnyak]

Thanks Alex, I was originally going to sort the sam files at the command line, but this is MUCH faster!

Vlad