How to Interpret Chromosome Names from

Question

[dec986]

I have downloaded data thus:

wget 'ftp://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.25.gz'

which gives strange chromosome names: NC_000001.10 and NC_000002.10, NC_000003.10

Can I interpret these chromosomes as 1, 2, and 3 respectively?

Answer 1

[Pierre Lindenbaum]

see https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_report.txt

# Sequence-Name Sequence-Role   Assigned-Molecule   Assigned-Molecule-Location/Type GenBank-Accn    Relationship    RefSeq-Accn Assembly-Unit   Sequence-Length UCSC-style-name
1   assembled-molecule  1   Chromosome  CM000663.1  =   NC_000001.10    Primary Assembly    249250621   chr1

use

bcftools annotate --rename-chrs

to change the chromosomes' names

Answer 2

[JC]

check https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25