shapeit2 pre-phasing error- empty hap file
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5.1 years ago
Mamta ▴ 460

HI all ,

iam pre-phasing dataset using shapit2, however i get empty hap file , with additional filename.snp.mm and filename.ind.mm. I was reading that this usually happens with missing snps/ind. But I have already removed that before using plink. Log file below:

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" Checking missingness and MAF... * 0 individuals with high rates of missing data (>5%)
* 0 SNPs with high rates of missing data (>5%)
* 55902 monomorphic SNPs
* 29232 missing genotypes automatically imputed at monomorphic SNPs * 9216 singletons SNPs Building graphs ... * 306 graphs / 1809544 segments / ~25 SNPs per segment / 61905592 transitions
* 0 haploids / 306 unrelateds / 0 duos / 0 trios * 612 founder haplotypes Sampling haplotypes Burn-in iteration [1/7] Burn-in iteration [2/7] Burn-in iteration [3/7] Burn-in iteration [4/7] Burn-in iteration [5/7] Burn-in iteration [6/7] Burn-in iteration [7/7] Pruning iteration [1/8]"

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Thanks, Mmata

GWAS shapeit2 pre-phasing • 2.3k views
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