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  • Bed file coordinate sorting

    Apparently, I don't quite understand how a bed file should be sorted. I can't quite figure out what's wrong.

    Code:
    bedops --ec --everything myData.bed > /dev/null
    May use bedops --help for more help.
    
    Error: in oncosnp.bed
    Bed file not properly sorted by first column.
    See row: 771
    
    cat myData.bed | awk 'NR>=769' | head
    9	138338321	138339032
    9	139327439	140167730
    10	69083	3368595
    10	367632	393272
    10	448018	448786
    10	703003	763714
    10	998193	999290
    10	1084691	1123868
    10	1368946	1369689
    10	1500525	1503838

    Any idea? How does the ordering rule work for bed files?

    A related question: when I used bedtools and use the "-sorted" flag, how should that bed file be sorted?

    Thanks in advance.
    Last edited by lethalfang; 05-18-2014, 07:06 PM.

  • #2
    You treated them as numbers, so they're in numeric order. However, they need to be in lexicographic order, since "10" as a word comes before "9" as a word (the normal order would be something like: 1, 10, 11 ... 19, 2, 3, ...). This will make more sense if you have chromosomes X and Y and/or MT (or are using UCSC chromosome names).

    Comment


    • #3
      Originally posted by lethalfang View Post
      A related question: when I used bedtools and use the "-sorted" flag, how should that bed file be sorted?
      Sort by chromosome (lexicograhic) then by position. Something like this will do

      Code:
      sort -k1,1 -k2,2n -k3,3n a.bed > asort.bed
      (In fact I suspect that for -sorted option to work, what matters is that chromosomes are in the same order in both files).

      By the way, if records within chromosomes are already sorted by position and so you just want to sort chromosomes, use the --stable option in sort. It will save quite some time for big files.

      Comment


      • #4
        You can use BEDOPS sort-bed to sort BED files:



        GNU sort is not as fast as sort-bed (even with various tricks, like --parallel and so forth) and it's easy to get the options wrong.

        Comment

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