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Library Htsjdk to query a vcf file
Entering edit mode
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.

Entering edit mode

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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