I did the inputation for missing SNP by MACH with the panel "hm3_r2_b36_fwd.CEU" or "CEU.r22.orig"
There was a FATAL ERROR——Please ensure that allele labels in pedigree are consistent with haplotype file...
It is confused me that whether the #snp(rsXXXX) in both my raw data and panel should be one-to-one correspondence. That is to say, they can not match the same label automatically.
How should I do In this case? (1) Match the #snp(rsXXXX) manually? OR (2) Simply do it without panel——mach1 -d sample.dat -p sample.ped --rounds 50 --states 200 --phase --compact
Please give some details about results of the two different methods above.Thanks