How To Fetch Chromosome Coordinates From Sequence
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6.1 years ago
lverarighi • 0

Hi, I have my VCF file with reference like ##contig=<id=gi|568815364|ref|nt_077402.3|,length=197666> and then the sequence in the body of the vcf began like this gi|568815364|ref|NT_077402.3| ......

As you could see I don't have the chrommosome, isted of that I have a reference, and in this way annovar didn't found any variant.

Someone know How could I have the crhomosome and the start and end position in the sequence?

I very appreciate your help

thank you

alignment next-gen • 1.2k views
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Entering edit mode
6.1 years ago
apa@stowers ▴ 580

What it looks like is that header and records have different capitalization, "nt_077402.3" vs "NT_077402.3". I would fix that first.

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