I am trying to use SAMtools Text Alignment Viewer, but I get a long line of Ns and not an output similar to what is shown here:
http://samtools.sourceforge.net/tview.shtml
I am using it as specified:
http://samtools.sourceforge.net/samtools.shtml
samtools tview <in.sorted.bam> [ref.fasta]
Does anyone know, if there are unix alternatives out there for viewing specific positions in bam files? I need to parse 1000bps on each side of 2 million positions.
OK, I got samtools tview to work, but given my task at hand, I probably still need an alternative given the many positions I have to parse.
http://samtools.sourceforge.net/tview.shtml
I am using it as specified:
http://samtools.sourceforge.net/samtools.shtml
samtools tview <in.sorted.bam> [ref.fasta]
Does anyone know, if there are unix alternatives out there for viewing specific positions in bam files? I need to parse 1000bps on each side of 2 million positions.
OK, I got samtools tview to work, but given my task at hand, I probably still need an alternative given the many positions I have to parse.