how to convert top/bot, or plus/minus strand to positive/negative strand

Question

[lilingjoyo]

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

[Paravee]

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?