how to convert top/bot, or plus/minus strand to positive/negative strand
0
0
Entering edit mode
4.4 years ago
lilingjoyo ▴ 40

I‘m trying to convert top/bot or plus/minus strand of Illumina genotype array to positive strand of reference genome. Because I want to do imputation which requires my genotype is based on positive strand.

Name    SNP ILMN Strand Customer Strand
1:100292476 [A/G]   TOP TOP
1:101064936 [A/G]   TOP TOP
1:103380393 [T/C]   BOT TOP
1:104303716 [T/C]   BOT TOP
1:104864464 [A/G]   TOP BOT
1:106737318 [A/C]   TOP BOT
1:109439680 [A/G]   TOP TOP
1:111119214 [T/C]   BOT BOT
1:114483147 [A/C]   TOP TOP

I used command convert_bim_allele.pl of GenGen:

convert_bim_allele.pl old.bim new.bim --intype ilmnab --outtype dbsnp --outfile new.bim 
Error: invalid allele designation (0/A/B expected based on --intype of ilmnab): <1  GSA-rs114420996 0   58814   A   G
genome • 2.1k views
ADD COMMENT
0
Entering edit mode

Hi. I know this is an old question, but have you ever found out how to convert illumina's top/bottom to pos/neg strand orientation? Does the 'convert_bim_allele.pl' script work?

ADD REPLY

Login before adding your answer.

Traffic: 1263 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