Hi,
I am a family of 7 related individual that I would like to do the haplotype analysis on chromesome 22. I used shapeit to run the analysis with my SNP data with this command:
shapeit --input-ped IL2RB_chr22.ped IL2RB_chr22.map \ --input-map IL2RB_genetic.map \ --input-ref 1000GP_Phase3_chr22.hap.gz \ 1000GP_Phase3_chr22.legend.gz \ 1000GP_Phase3.sample \ --duohmm \ --output-max IL2RB_chr22_test2.haps IL2RB_chr22_test_phased2.smaple \ --thread 8
it return me with the error like this: ERROR: Reference and Main panels are not well aligned: * #Missing sites in reference panel = 131 * #Misaligned sites between panels = 3136 * #Multiple alignments between panels = 0
I tried to flip the data, but still return the same Error, what should I do? Many thanks in advance!
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written
by
chenpu2013 •
1 answer
Please see my answer: A: Strand Alignment in ShapeIt -- "Reference and Main panels are not well aligned"
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Have you solved the problem? I also encountered the same problem. look forward to your reply
I have been trying to solve this same issue for about 2 weeks now. I have done some troubleshooting and the positions in my sample file are in the haplotype reference panel. I can’t figure how my reference and main panels can be misaligned when they have 80% of the same sites between the two of them (according to my tests with my own scripts).