Phasing using SHAPEIT


I need to use SHAPEIT for phasing only since I will conduct CH (compound heterozygous) analysis for recessive rare variant.. I will not perform imputation. 

I am running SHAPEIT, and I see in the log file it says:

Parameters :
  * Seed : 1442251531
  * Parallelisation: 12 threads
  * Ref allele is NOT aligned on the reference genome
  * MCMC: 35 iterations [7 B + 1 runs of 8 P + 20 M]

I am still able to get *haps file for haplotypes for CH, however, I am not sure if I am doing correctly.

Is it ok to have “Ref allele is NOT aligned on the reference genome” notice on my log file?…


I have one more question..

My input file is plink PED/MAP format, and on the SHAPEIT website (, it says that SHAPEIT considers “0” as missing data.

And they suggested people to change the missing data character to “N” for example, use –missing-code options as follows:

shapeit --input-ped chr20.unphased.ped -M chr20.gmap.gz --output-max chr20.phased --missing-code N

However, –missing-code N gives me an error “ERROR: Non biallelic site pos=24118582 a=0”

So, I did not use –missing-code N and run SHAPEIT:

shapeit –input-ped chr20.unphased.ped -M chr20.gmap.gz –output-max chr20.phased

Would that be ok?


Thank you so much,



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