sam to bam

[kwtennis311]

I was sure this had been asked earlier, but could not find. Does anyone have a script to convert files from sam to bam format?

Thanks

[quinlana]

Use samtools view. The -S indicates the input is in SAM format and the "b" indicates that you'd like BAM output.

samtools view -Sb  <SAMFILE>  >  <BAMFILE>

[Lee Sam]

You can also use samtools import command (this is what I am using), which does this exact thing.