On 8 May 2016, at 17:27, Peter Chovanec <peter.chova...@babraham.ac.uk> wrote:
> Why doesn't this work:
>
> samtools view sample.bam 2:33050509-33154206 -U without-region.sam
>
> or
>
> samtools view -b sample.bam 2:33050509-33154206 -o other_stuff.bam -U
> without-region.bam
You don't say what you were expecting to have happen, but presumably, like the
biostars poster, you were hoping to get the reads outside the
2:33050509-33154206 region (i.e., elsewhere on chromosome 2 and anywhere on any
other chromosome under the sun).
If you think about how specifying a region like 2:33050509-33154206 works, you
will see why this didn't do what you hoped for. Samtools view uses the index
to jump straight to this region and never looks at the reads outwith, so such
reads are not scanned or added to the output.
If you used some filtering options with this:
samtools view -b -f 0x10 -o reverse.bam -U forward.bam sample.bam
2:33050509-33154206
then you would get reads in both output files. This writes
mapped-to-reverse-strand reads in 2:33050509-33154206 to one file and
forward-mapped reads in that region to the other file.
This is described in the man page as
-U FILE
Write alignments that are not selected by the various filter options to FILE.
When this option is used, all alignments (or all alignments intersecting the
regions specified) are written to either the output file or this file, but
never both.
Note the part in parentheses. Probably this needs to spell out what it means
by "filter options" more clearly -- region arguments aren't part of them! --,
but see also the introduction to samtools view in the man page. Perhaps it
would also help if samtools view emitted a message if both -U and a region are
given.
John
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