Samtools sort error

Question

[V]

Hello,

I've got a SAM file that was aligned using HISAT2, I've converted it into a BAM file using samtools view, I then wanted to sort it using samtools sort and this output comes out and just keeps going and going so I stop it.

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The ultimate goal is that I want to convert my sam file into a bam file and then index it to help with viewing. Would anyone know of a way around this or how to fix this?

[John]

I almost feel sorry for the Biostars syntax highlighter :(

Write this stuff out to a file with "> sorted.bam"

[Istvan Albert]

I am pleased that the site did not blow up to pieces when a BAM file is posted - though the RSS feed did.

As for the answer, what you have there is a binary, BAM file that is being output to your screen. Redirect it or use the manual to see how to save that into a file rather than a screen.

[WouterDeCoster]

samtools has very convenient help information on the command line. Just type samtools or samtools sort to get usage information. In addition, which version are you using?

[V]

Yes yes lets all troll the ubuntu newbie :) Thanks! Got it to work.

[GenoMax]

We promise not to .. only if use ADD REPLY/ADD COMMENT when responding to existing posts next time :) This helps keep threads logically organized.

[V]

Sorry...growing pains!

Answer 1

[John Marshall]

Try rereading the samtools sort documentation (see man samtools, or here for the current version) and checking that you are giving the sort options and arguments correctly.

Answer 2

[Johanna Schott]

Don't worry! This is how a bam file should look like:) It is a binary version of the "human readable" sam file. If I look at the first few lines of one of my own bam files with "head mysample.bam", what I see looks very similar to your output. If you want to see the "human readable" format again, use samtools: "samtools view mysample.bam | head" should show you the first lines of your bam file as you had it in the original sam file. As John suggested, write the output to a file and not to the screen.