This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Did dbSNP not get the memo about hg38 chromosome names?

I thought everyone was switching over to 'chr1' style chromosome names for hg38. Why do I still see the Ensembl-style chromosome names here?

tabix -l ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/VCF/00-All.vcf.gz
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
X
Y
MT
hg38 grch38
• 3,442 views • link
updated by DG DG • written by Jeremy Leipzig Jeremy Leipzig

I never heard that there was any kind of consensus, and FWIW I'd have argued that "chr" prefixes are dumb and should go away. ;)

• 0 views • link
written by Chris Miller Chris Miller

1 answer

Last I had heard there was a failure with standardizing on the chromosome names as planned. I thought NBCI was going to follow the UCSC convention though, but Ensemble wasn't switching their naming scheme due to worry about breaking existing pipelines, etc.

• 0 views • link
written by DG DG

Log in to answer this question.

More posts like this