Question: how to convert top/bot, or plus/minus strand to positive/negative strand
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lilingjoyo • 40 wrote:
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
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modified 2.7 years ago
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WouterDeCoster ♦ 45k
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written
2.7 years ago by
lilingjoyo • 40