0
$\begingroup$

This question was also asked on Biostars

In other words, are NCBI37 and hg19 synonymous? I can't find much information for what NCBI37 is in a human (not mouse) genome.

The VCF is from a lab sequencing human genomes, and they're no longer able to be reached out to. I can't provide a link to NCBI37 because I don't know what it is and I can't find much information on it.

Relevant line from VCF: "##reference=NCBI37"

Here is part of the VCF header:

##fileformat=VCFv4.2
##source=apt-format-result:2.10.2
##reference=NCBI37
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1>
##contig=<ID=10>
##contig=<ID=11>
##contig=<ID=12>
##contig=<ID=19> [omitted some chromosomes for brevity]
##contig=<ID=2>
##contig=<ID=20>
##contig=<ID=MT>
##contig=<ID=X>
##contig=<ID=Y>
$\endgroup$
0

1 Answer 1

1
$\begingroup$

Most likely yes, they are the same.

However, "NCBI37" is an odd/unusual notation, because it doesn't indicate the species (human / mouse). Assuming it's a human genome (based on you comparing it to hg19 rather than mm19, or something else), then the correct name for the NCBI reference should be GRCh37.

As it's a different name, we can only make guesses as to what the people who generated the VCF meant. You'll need to talk directly to them in order to be sure.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.