This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What Is Practical Issues For Samtools Not Able To Sort The Sam File Directly?

I was just wondering why we always needs to convert .sam to .bam and the sort it and convert back to .sam Any programming bottle necks to handle .sam file directly for this?

samtools sort sam bam
• 5,215 views • link
updated by sowmya.kuruganti • sowmya.kuruganti • written by Rm Rm

If you convert a sorted .bam file to .sam file, are you sure the .sam file is sorted?

• 0 views • link
written by Chen Sun Chen Sun

yes, the samtools view command output the records in the bam file in the order they are stored.

• 0 views • link
written by Istvan Albert Istvan Albert

3 answers

Sorting is a resource consuming operation, the binary formats will sort much faster.

• 0 views • link
written by Istvan Albert Istvan Albert

Why would you convert back to sam? Leave things in .bam as much as possible. You probably only need to eyeball exerpts of your .sam file. pipe samtools view into something else if you have to run awk or grep or something like that on a ,bam file

• 0 views • link
written by swbarnes2 swbarnes2

Or instead of using awk/grep on the output of samtools view, bamtools can be helpful to query bams directly.

• 0 views • link
written by Steve Lianoglou Steve Lianoglou

I did all the piping and to get the sorted sam. I have methylation data (bismark generated sam file); Some of the R packages (say methylKit) need sorted SAM files only.

• 0 views • link
written by Rm Rm

You could use Picard's SortSam tool to just sort the .sam file directly.

• 0 views • link
updated by Ram Ram • written by sowmya.kuruganti • sowmya.kuruganti

Log in to answer this question.

More posts like this