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  • Library Htsjdk to query a vcf file

    I'm using
    Code:
    VCFFileReader file= new VCFFileReader(file.vcf, file.vcf.gz.tbi, true)
    to open a file and then
    Code:
     CloseableIterator<VariantContext> vc = file.query("10", 77162995, 131048262)
    to query specific regions of the file.
    The problem is that when I choose a region in the middle or the end of the chromosome the method doesn't return anything. For the region starting at position 77162995 and end at 131048262 it doesn't work.

  • #2
    Which organism is it? What is actually the length of your chromosome 10? For Human, it should work, for mouse, since you are requesting out of the chromosome 10, I am not surprised it doesn't...
    Last edited by SylvainL; 02-23-2016, 05:09 AM.

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    • #3
      It's for human. Chromosome is from 47588 to 133787425. If I search in the beginning of the chromosome, it gives no problem. But if I search in the middle it does not return anything.
      Last edited by binfoUser; 02-23-2016, 05:16 AM.

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      • #4
        Where did you get the genome? ENSEMBL (names of chromosomes without "chr"), UCSC (then it should be "chr10")?

        Does this function work if you request for example?
        vc = file.query("10", 995, 48262)

        edit: our posts got crossed...

        Did you try to request a shorter sequence?

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        • #5
          Yes it does. The first result is 47588 and the last 48249.

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          • #6
            Are you sure you have variant in this region?

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            • #7
              Each line represents a variant found in the DNA sequence, so if I specify a region present in the file the algorithm has to return that region.
              It's strange not to work for the whole file.
              Last edited by binfoUser; 02-23-2016, 10:00 AM.

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