This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Better place to download dbSNP than official ftp site?

I need to download dbSNP of VCF format. If I download the last release b154 from
https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.38.gz
The problem is the contig name is not chromosome, but something like "NC_000001.11", "NT_113793.3", "NW_019805489.1".

If I dowload older version b151 from
https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/All_20180418.vcf.gz
The problem is no contig in header, I added by hand for example ##contig=<ID=1>. But there is one value MTP in INFO field with no definition in header. Does anyone know the definition so I can add to header.

dbsnp
• 4,050 views • link
written by MatthewP MatthewP

1 answer

The problem is the contig name is not chromosome, but something like "NC_000001.11"

rename the chromosomes with bcftools annotate. This file will help to get the two-columns file: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_assembly_report.txt

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this