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  • CONTRA vcf results

    hi, i'm learning the CONTRA, by using the test datas downloaded on sourceforge, command as follows { Python-2.7/python CONTRA.v2.0.3/contra.py -t 0247401_D_BED_20090724_hg19_MERGED.bed -s P0667T_GATKrealigned_duplicates_marked.bam -c P0667N_GATKrealigned_duplicates_marked.bam -f human.fa -o outdir };
    here are the programs in it:
    1. Python-2.7
    2. R version 2.10.0
    3. samtools version: 0.1.8
    4. BEDTools-Version-2.11.2

    No error reports during processing(just like the web shows http://sourceforge.net/projects/cont.../Test%20files/). 3 files in the '/outdir/table' dir (CNATable.10rd.10bases.20bins.vcf; CNATable.10rd.10bases.20bins.DetailsFILTERED.txt; CNATable.10rd.10bases.20bins.txt), there are no cnv information in vcf file, only this description (
    ##fileformat=VCFv4.0
    ##reference=1000GenomesPilot-NCBI36
    ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"
    ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"
    ##ALT=<ID=CNV,Description="Copy number variable region"
    #CHROM POS ID REF ALT QUAL FILTER INFO)
    dose anyone know why?? thanks for help~

  • #2
    I'm at the same point... does anyone know what's going on?

    Comment


    • #3
      I had the same issue and wrote to the developer. He said he would have checked that but there have been no updates since then.
      I've tried to run CONTRA with python debugger, I remember there was a bug in some intermediate file that was not created, but then gave up and worked with bed-like outputs.

      d

      Comment


      • #4
        Originally posted by dawe View Post
        I had the same issue and wrote to the developer. He said he would have checked that but there have been no updates since then.
        I've tried to run CONTRA with python debugger, I remember there was a bug in some intermediate file that was not created, but then gave up and worked with bed-like outputs.

        d
        Thank you dawe.

        It's a pity. The program looks very nice and it fits perfectly to my bunch of samples! I've also written to the developer and well... waiting !

        Anyway if you could shed some light on how to work with CNVs with this "bed-like outputs" I'll be very grateful. One of the hardest things when you're a rookie (I think) is to have good judgment about which tools to use...

        Comment


        • #5
          Hi,

          I have the same issue and can't figure out what the issue is. Did someone solve this problem? Is there another way to get the results without the .vcf file?

          Thanks

          Comment

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