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Library Htsjdk to query a vcf file
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13 months ago
onemoreuser • 10

I'm using:

VCFFileReader file= new VCFFileReader(file.vcf, file.vcf.gz.tbi, true)

to open a file and then

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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Are there any records in this interval? If there aren't any it might be normal to return nothing (I haven't tried...)

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