[Biopython] [Samtools-help] SAM to BAM
Peter Cock
p.j.a.cock at googlemail.com
Mon Oct 17 13:06:58 UTC 2011
On Mon, Oct 17, 2011 at 1:11 PM, Mic <mictadlo at gmail.com> wrote:
> Hello,
> Is there a way to convert SAM file to sorted BAM file and generate also BAI
> file with pysam?
> Thank you in advance.
With samtools at the command line,
samtools view -b -S example.sam | samtools sort - example
samtools index example.bam
I know you can easy call samtools from pysam, not sure if you
can do the pipe trick to avoid extra steps:
samtools view -b -S example.sam > example_unsorted
samtools sort example_unsorted.bam example
rm example_unsorted.bam
samtools index example.bam
Peter
More information about the Biopython
mailing list