This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Plink Error Message :Error: Badly Defined Segment, 2 > 1

Hi

I have this error message when run plink

Options in effect: --noweb --cnv-list population_cnv.cnv --cnv-make-map

Reading segment list (CNVs) from [ population_cnv.cnv ]

ERROR: Badly defined segment, 2 > 1

What does this error mean ?? This is some example of my data

FID    IID    CHR    BP1    BP2    TYPE    SCORE    SITE
CEU1    1    1    17082190    17140083    3    100    0
CEU2    2    1    25461733    25534799    0    100    0
CEU3    3    1    34875241    34880863    1    100    0
CEU4    4    1    72538673    72583736    0    100    0
plink cnv
• 2,462 views • link
updated by zx8754 zx8754 • written by naktang1 • naktang1

1 answer

From plink code you can see that it tests if the start-BP1 is bigger than stop-BP2 position. Check your CNV file.

  if ( p1 > p2 ) 
    error("Badly defined segment, " + bp1 + " > " + bp2);
• 0 views • link
written by zx8754 zx8754

Log in to answer this question.

More posts like this