Library Htsjdk to query a vcf file

[binfoUser]

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.

[SylvainL]

Are you sure you have variant in this region?

[binfoUser]

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

[SylvainL]

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?

[binfoUser]

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.

[SylvainL]

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...

[binfoUser]

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.