How To Fetch Chromosome Coordinates From Sequence

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

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updated 9.6 years ago by apa@stowers

• written 9.6 years ago by lverarighi •

1 answer

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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written 9.6 years ago by apa@stowers

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