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  • binfoUser
    replied
    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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  • SylvainL
    replied
    Are you sure you have variant in this region?

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  • binfoUser
    replied
    Yes it does. The first result is 47588 and the last 48249.

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  • SylvainL
    replied
    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?

    Leave a comment:


  • binfoUser
    replied
    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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  • SylvainL
    replied
    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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  • binfoUser
    started a topic Library Htsjdk to query a vcf file

    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.

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