How To Fetch Chromosome Coordinates From Sequence

Question

[lverarighi]

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

Answer 1

[apa@stowers]

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