How to update rsid given chromosome number, chr position, a1 and a2
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3.1 years ago
paria ▴ 90

Hi, To update the SNP ID of my summary stat file I have some questions: First, I have created a text file from the summary stat file with the following information 1 1118275 vh_1_1108138 G A
1 1120431 vh_1_1110294 A G
1 1135242 rs9729550 C A
1 1140435 rs1815606 A C
1 1163804 rs7515488 A G
1 1165310 rs11260562 A G
1 1173611 rs6697886 A G
1 1186502 rs6603785 T A
1 1194804 rs11804831 G A
1 1218086 rs6603788 A G

I need to update the rsID to have the consistent format (as you see some have vh_.. format). Then, I downloaded the dbsnp vcf and chosed the following columns

1 10019 rs775809821 TA T
1 10039 rs978760828 A C
1 10043 rs1008829651 T A
1 10051 rs1052373574 A G
1 10051 rs1326880612 A AC
1 10055 rs768019142 T TA
1 10055 rs892501864 T A
1 10063 rs1010989343 A C
1 10077 rs1022805358 C G

1) I was wondering how could I merge the columns to update the rsID in the first text file? 2) I noticed that the second column has different format (chromosome position). I don't know whether it causes a problem. If yes, how could I update it too. I appreciate any help

SNP ID • 677 views

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