SNP candidates

2005-11-14
2013-04-18
  • I installed the Linux und Solaris binary 1.6. When I try
    to run the new feature 'SNP canditates', I am getting
    the error message:
    Error: can't read "basea(N)": no such element in array
    (see details below). Any idea how to correct this?

    Tim Strom
    Institute of Human Genetics
    GSF and Technical University
    Munich

    can't read "basea(N)": no such element in array
    can't read "basea(N)": no such element in array
        (reading value of variable to increment)
        invoked from within
    "incr basea([lindex $b 2])"
        (procedure "display_bases" line 14)
        invoked from within
    "display_$type $d $xpos"
        (procedure "::haplo::display" line 39)
        invoked from within
    "::haplo::display $h"
        (procedure "CandidateSNPs2" line 25)
        invoked from within
    "CandidateSNPs2 1 .snps .snps.id"
        invoked from within
    ".snps.ok.ok invoke"
        ("uplevel" body line 1)
        invoked from within
    "uplevel #0 [list $w invoke]"
        (procedure "tk::ButtonUp" line 22)
        invoked from within
    "tk::ButtonUp .snps.ok.ok"
        (command bound to event)

     
    • James Bonfield
      James Bonfield
      2005-11-16

      What consensus algorithm and quality cutoff are you using? I've found that enabling IUBC codes really breaks SNP Candidates (so I'll fix that), but otherwise try as I may I cannot get an N to appear in any of my sequences.

      James

       
    • TimStrom
      TimStrom
      2005-11-23

      Thank you for the anwser. SNP candidates crashes
      when the sequences contains IUBC codes or Ns.
      We use the ABI base caller that uses IUBC code and
      add Ns for known polymorphisms. As I understand
      SNP candidates can not recognize heterozygous bases
      because the quality is usually very low?

       
    • James Bonfield
      James Bonfield
      2005-11-28

      Please try the latest CVS copy and let me know if it cures the problem.

      http://cvs.sourceforge.net/viewcvs.py/\*checkout*/staden/staden/src/haplo/haplo.tcl?content-type=text%2Fplain

      James