ARS-UCD, UMD and Btau reference SNP map files

Question

[PeterKW]

Hi everyone,

I would like to download the current Bos taurus reference map files from the ARS-UCD, UMD and Btau assemblies with the reference SNP numbers, chromosome and position. I have tried to search on the NCBI website (https://www.ncbi.nlm.nih.gov/assembly/organism/9913/latest/) but I can't locate the information. I will greatly appreciate a link to this information.

Thanks, Peter

[GenoMax]

Ensembl has VCF for B. taurus available in this folder.

[PeterKW]

Thanks, GenoMax. Is this the ARS-UCD1.2 assembly?

[GenoMax]

Correct (ARS-UCD1.2 (GCA_002263795.2)).

[PeterKW]

GenoMax thanks a lot.

[PeterKW]

Hi Everyone,

I thought I could share this here for those who might be looking for this information. I found this and this useful to access the Bos taurus BTAU and UMD SNP map files, respectively.

In the EMBL-EBI EVA browser, I can only browse one chromosome at a time. Anyone with a solution around this or an alternative database where I can download a full UMD 3.1.1 map file with reference SNPs, chromosomes and SNP positions (at least)?

Thanks.

[Mandeep]

Hello Everybody - Where I can download a full UMD 3.1.1 map file and ARS-UCD 1.2 map file?

I have encountered a problem of genotype data merging for overlapped SNPs by chromosome and position. However, these two data files have different names. Map file 1 is an older one that used previous genome assembly with SNP names as follows:

File1.map 0 rs42206466 0 148304112 1 rs41609588 0 135098 1 rs108982244 0 267940 1 rs43703977 0 393248 1 rs110887329 0 471078 1 rs29015852 0 516404 1 rs110936909 0 571340 1 rs108981857 0 845494 1 rs110467572 0 883895 1 rs109719982 0 905632

I have another file that was genotyped recently using ARS 1.2 and its map file has different snp Names. However, the literature says file1 and file 2 have close to 30k overlapped variants. The second mapfile (file2.map) has different name for SNPs as it used an updated version of the 2018.

File2.map 1 chr3_133498 0 649094 1 BovineHD0100000005 0 655346 1 BovineHD0100000035 0 761316 1 Hapmap43437-BTA-101873 0 776231 1 BovineHD0100000042 0 790905 1 BovineHD0100000043 0 792193 1 BovineHD0100000048 0 799951 1 BovineHD0100000051 0 805126 1 BovineHD0100000057 0 824172

How can I merge these two files with overlapped variants? What would be the updated name of SNPs for file 1 in ARS 1.2 version so that I can merge file1.map and file2.map based on overlapped variants by chromosome and position. Or if there is any other alternative way-outs to handle this problem?

[PeterKW]

Hi @Mandeep,

If I get your question right, File 1 has the Reference SNP cluster ID while File 2 has the SNP "commercial names" which sometimes are different for different genotyping companies. This means for every SNP there is an RS ID and name(s). To get one file with both the RS and names per SNP you can use the chromosome numbers and positions to match the two in say R or any other program.

I got the ARS 1.2 map file with RS IDs here and one with SNP names here. I found these helpful.

I hope this helps.