Thank you. Now it makes sense why it works with the -L option. On 09/05/16 10:11, John Marshall wrote: > 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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