Recently , I studied Illumina chicken 60k SNP chip. The orignal data was writed in plink map and ped file. My idea are as follows:
- use plink to QC
- convert the data after QC to vcf format
- use beagle4 to genotype imputation
- do some analysis
While in step 3, the beagle4 does not support for the AB format. I tried to use the gengen (refrence to http://gengen.openbioinformatics.org/en/latest/tutorial/coding/) to convert AB to ACTG. The gengen needs the snptable which has 4 columns like
Name SNP ILMN Strand Customer Strand
200003 [T/C] BOT TOP
200006 [A/G] TOP BOT
200047 [T/C] BOT TOP
200050 [C/G] TOP BOT
200052 [T/A] BOT TOP
I may got the first 3 columns but the last column data was gone. So here I want to ask you the way to got the data or the way to genotype impute without converting AB to ACTG . Look forward to your favourable reply.
shoud i add a comment to up my post?