dbsnp with ucsc chromosome annotations

Question

[rk.khayami94]

I wanted to download the latest version of dbsnp from https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.39.gz

I took a quick look at the file and saw that the chromosome names are like NC_000001.11 but I need them to be in ucsc format (e.g. chr1).

Is there any sites to download the latest version of dbsnp with UCSC chromosome nomenclature? I know GATK bundle has one but it's old.

Here is a snippet of the data

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
NC_000001.11    10001   rs1570391677    T       A,C     .       .       RS=1570391677;dbSNPBuildID=154;SSR=0;PSEUDOGENEINFO=DDX11L1:100287102;VC=SNV;R5;GNO;FREQ=KOREAN:0.9891,0.0109,.|SGDP_PRJ:0,1,.|dbGaP_PopFreq:1,.,0;COMMON

Answer 1

[Pierre Lindenbaum]

replace the chromosome names: with bcftools annotate bcftools annotate --rename-chrs and something like https://github.com/dpryan79/ChromosomeMappings/blob/352087c1f859ff363c735294070acaf49054c600/GRCh37_NCBI2UCSC.txt

[rk.khayami94]

Now when I want to index the file I get this error:

Unsorted positions on sequence #590: 145974 followed by 11
tbx_index_build failed: dbsnp155ucsc.vcf.gz