I am using below scripts:

java -jar conform-gt.24May16.cee.jar ref=Chr01.merged_files_Miss_new.vcf.gz gt=batch1-8_450k_edited.beagle.39474SNPs_new.vcf.gz chrom=1 match=ID out=mod.chr01.consistent

to align my input file to the reference (unphased yet).

Below is the error message:

Below is the error message: Exception in thread "main" java.lang.IllegalArgumentException: Duplicate marker Chr01.merged_files_Miss_new.vcf.gz]: 1 1 1_1.9e+07 C T at conform.ConformMarkers.<init>(ConformMarkers.java:62) at conform.ConformMain.<init>(ConformMain.java:108) at conform.ConformMain.main(ConformMain.java:97)

Based on the error message, I guess that there are duplicate markers or triallelic SNPs. However, I did not find any duplicated markers in reference and target dataset based on my bin files. I was wondering whether I need to phase the reference panel first.

My bin file of reference panel, with unphased genotype/GT

1       1_42    0       42      A       G
1       1_49    0       49      G       C
1       1_64    0       64      C       T
1       1_65    0       65      G       A
1       1_67    0       67      T       C
1       1_76    0       76      G       A
1       1_87    0       87      T       G
1       1_102   0       102     C       T
1       1_107   0       107     A       T
1       1_123   0       123     A       T