Dear colleagues - 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
1 BovineHD0100000066 0 842891
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?
