Samtools Rmdup, file output empty

Question

[mmukhame321]

Hello,

I am trying to output a file that removed PCR duplicates by using rmdup command. My file is single-ends.

I put this into my terminal: samtools rdup [-s] input_path_file_directory > output_path_file_and_file_name.bam

It makes the file, the only thing is that the file is empty. Any ideas why?

Thanks

[iraun]

Are you using this command?

samtools rmdup -s input.bam output.bam

You don't need '>' symbol to get the output bam.

[Nicola Casiraghi]

> explains empty output.

[iraun]

Exactly :-)

[mmukhame321]

Thank you! I overlooked that, and got the results I needed!

Answer 1

[Nicola Casiraghi]

samtools rmdup -s input.bam out.bam

input.bam must be sorted (samtools sort).