Samtools view -f issue

[marco12345]

Hi,

I am trying to delete the unpaired reads from a BAM file. I tried with:

$ samtools view -f1 /input_file.bam > /output_file.bam

The resulting output is more than two times the sizes of the input, which I do not understand being the same file with less data.

Could someone please helo me? Also alternatives way to do the same process are welcome!

I am using samtools 0.1.18 on Terminal (Mac OSX)

[Richard Finney]

It's producing SAM (not BAM) output. SAM is uncompressed text, BAM is compressed binary so it is smaller.
Try the -b parameter to produce bam output.

[marco12345]

Now that was a stupid mistake i made! And I lost a morning trying to modify the most absurd parameters of the file and options of the "view"!!

Thanks a lot Richard