How to update rsid given chromosome number, chr position, a1 and a2
0
0
Entering edit mode
14 months ago

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 10067 rs1489251879 T TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
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 • 367 views
ADD COMMENT

Login before adding your answer.

Traffic: 1399 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6